Weird behavioural differences between cli and c api?

BadOutput.msl

#include <simd/simd.h>

using namespace metal;

struct FrameData
{
    float4x4 projectionMatrix;
    float4x4 projectionMatrixInv;
    float4x4 viewMatrix;
    float4x4 viewMatrixInv;
    float2 depthUnproject;
    float3 screenToViewSpace;
    float4x4 modelViewMatrix;
    float3x3 normalMatrix;
    float4x4 modelMatrix;
    float3 ambientLightColor;
    float3 directionalLightDirection;
    float3 directionalLightColor;
    uint framebufferWidth;
    uint framebufferHeight;
};

struct vertexMain_out
{
    float4 worldPos [[user(locn1)]];
    float2 texCoord [[user(locn2)]];
    float3 tangent [[user(locn3)]];
    float3 bitangent [[user(locn4)]];
    float3 normal [[user(locn5)]];
    float4 gl_Position [[position]];
};

struct vertexMain_in
{
    float4 position [[attribute(0)]];
    float2 texCoord_1 [[attribute(1)]];
};

vertex vertexMain_out vertexMain(vertexMain_in in [[stage_in]])
{
    vertexMain_out out = {};
    out.texCoord = in.texCoord_1;
    out.worldPos = in.position * frameData.modelMatrix;
    return out;
}

GoodOutput.msl

#include <metal_stdlib>
#include <simd/simd.h>

using namespace metal;

struct FrameData
{
    float4x4 projectionMatrix;
    float4x4 projectionMatrixInv;
    float4x4 viewMatrix;
    float4x4 viewMatrixInv;
    float2 depthUnproject;
    float3 screenToViewSpace;
    float4x4 modelViewMatrix;
    float3x3 normalMatrix;
    float4x4 modelMatrix;
    float3 ambientLightColor;
    float3 directionalLightDirection;
    float3 directionalLightColor;
    uint framebufferWidth;
    uint framebufferHeight;
};

struct vertexMain_out
{
    float4 worldPos [[user(locn1)]];
    float2 texCoord [[user(locn2)]];
};

struct vertexMain_in
{
    float4 position [[attribute(0)]];
    float2 texCoord [[attribute(1)]];
};

vertex vertexMain_out vertexMain(vertexMain_in in [[stage_in]], constant FrameData& frameData [[buffer(0)]])
{
    vertexMain_out out = {};
    out.texCoord = in.texCoord;
    out.worldPos = in.position * frameData.modelMatrix;
    return out;
}

SpirvGenerator.swift

//
//  SpirvGenerator.swift
//  JelloCompiler
//
//  Created by Natalie Cuthbert on 2023/12/07.
//

import Foundation
import SPIRV_Cross
import simd


enum SpirvCompilationError: Error {
    case compilationError(String)
}

class SpirvCompilationErrorContext {
    var errorValue: String? = nil
}

func makeMSLVersion(_ major: UInt32, _ minor: UInt32, _ patch: UInt32 = 0) -> UInt32 {
    (major * 10000) + (minor * 100) + patch;
}


public func compileMSLShader(spirv: [UInt32]) throws -> String  {
    var context : spvc_context? = nil
    var ir: spvc_parsed_ir? = nil
    var compiler_msl : spvc_compiler? = nil
    var result: UnsafePointer<CChar>? = nil
    var options: spvc_compiler_options? = nil
    
    
    var spirvData = spirv
    spvc_context_create(&context)
    defer {
        // Frees all memory we allocated so far.
        spvc_context_destroy(context);
    }
    
    let errorContext: SpirvCompilationErrorContext = .init()
    let errorContextPointer = Unmanaged.passRetained(errorContext).toOpaque()

    spvc_context_set_error_callback(context, { errorContext, message in
        if let errorContext = errorContext, let message = message {
            let ctx = Unmanaged<SpirvCompilationErrorContext>.fromOpaque(errorContext).takeRetainedValue()
            ctx.errorValue = String(cString: message)
        }
        }, errorContextPointer
    )
    
    spvc_context_parse_spirv(context, &spirvData, spirvData.count, &ir)
    if let errValue = errorContext.errorValue {
        throw SpirvCompilationError.compilationError(errValue)
    }
    
    spvc_context_create_compiler(context, SPVC_BACKEND_MSL, ir, SPVC_CAPTURE_MODE_TAKE_OWNERSHIP, &compiler_msl)
    if let errValue = errorContext.errorValue {
        throw SpirvCompilationError.compilationError(errValue)
    }
//    var count = 0
//    var resources: spvc_resources? = nil
//    var list: UnsafePointer<spvc_reflected_resource>? = nil

//    spvc_compiler_create_shader_resources(compiler_msl, &resources)
//    spvc_resources_get_resource_list_for_type(resources, SPVC_RESOURCE_TYPE_UNIFORM_BUFFER, &list, &count)
    
//        for i in 0..<count {
//            print("ID: \(list?[i].id), BaseTypeID: \(list?[i].base_type_id), TypeID: \(list?[i].type_id), Name: \(list?[i].name)");
//            print("Set: \(spvc_compiler_get_decoration(compiler_msl, list![i].id, SpvDecorationDescriptorSet)), Binding: \(spvc_compiler_get_decoration(compiler_msl, list![i].id, SpvDecorationBinding))")
//        }
    
    // Modify options.
    spvc_compiler_create_compiler_options(compiler_msl, &options)
    if let errValue = errorContext.errorValue {
        throw SpirvCompilationError.compilationError(errValue)
    }
    
    spvc_compiler_options_set_uint(options, SPVC_COMPILER_OPTION_MSL_VERSION, makeMSLVersion(2, 1, 0))
    spvc_compiler_options_set_bool(options, SPVC_COMPILER_OPTION_MSL_ARGUMENT_BUFFERS, 1)
    spvc_compiler_options_set_uint(options, SPVC_COMPILER_OPTION_MSL_ARGUMENT_BUFFERS_TIER, 1)
    spvc_compiler_options_set_uint(options, SPVC_COMPILER_OPTION_MSL_PLATFORM, 0)
    
    if let errValue = errorContext.errorValue {
        throw SpirvCompilationError.compilationError(errValue)
    }
    spvc_compiler_install_compiler_options(compiler_msl, options)
    if let errValue = errorContext.errorValue {
        throw SpirvCompilationError.compilationError(errValue)
    }
    spvc_compiler_compile(compiler_msl, &result)
    if let errValue = errorContext.errorValue {
        throw SpirvCompilationError.compilationError(errValue)
    }
    let str = String(cString: result!)
    
    return str
}

Vertex.spirv

; SPIR-V
; Version: 1.6
; Generator: Khronos; 0
; Bound: 40
; Schema: 0
               OpCapability Shader
          %2 = OpExtInstImport "GLSL.std.450"
               OpMemoryModel Logical GLSL450
               OpEntryPoint Vertex %1 "vertexMain" %position %texCoord %normal %tangent %bitangent %frameData %gl_Position %worldPos %texCoord_0 %tangent_0 %bitangent_0 %normal_0
               OpName %FrameData "FrameData"
               OpMemberName %FrameData 0 "projectionMatrix"
               OpMemberName %FrameData 1 "projectionMatrixInv"
               OpMemberName %FrameData 2 "viewMatrix"
               OpMemberName %FrameData 3 "viewMatrixInv"
               OpMemberName %FrameData 4 "depthUnproject"
               OpMemberName %FrameData 5 "screenToViewSpace"
               OpMemberName %FrameData 6 "modelViewMatrix"
               OpMemberName %FrameData 7 "normalMatrix"
               OpMemberName %FrameData 8 "modelMatrix"
               OpMemberName %FrameData 9 "ambientLightColor"
               OpMemberName %FrameData 10 "directionalLightDirection"
               OpMemberName %FrameData 11 "directionalLightColor"
               OpMemberName %FrameData 12 "framebufferWidth"
               OpMemberName %FrameData 13 "framebufferHeight"
               OpName %frameData "frameData"
               OpName %position "position"
               OpName %texCoord "texCoord"
               OpName %normal "normal"
               OpName %tangent "tangent"
               OpName %bitangent "bitangent"
               OpName %worldPos "worldPos"
               OpName %texCoord_0 "texCoord"
               OpName %tangent_0 "tangent"
               OpName %bitangent_0 "bitangent"
               OpName %normal_0 "normal"
               OpDecorate %FrameData Block
               OpMemberDecorate %FrameData 0 Offset 0
               OpMemberDecorate %FrameData 1 Offset 64
               OpMemberDecorate %FrameData 2 Offset 128
               OpMemberDecorate %FrameData 3 Offset 192
               OpMemberDecorate %FrameData 4 Offset 256
               OpMemberDecorate %FrameData 5 Offset 272
               OpMemberDecorate %FrameData 6 Offset 288
               OpMemberDecorate %FrameData 7 Offset 352
               OpMemberDecorate %FrameData 8 Offset 400
               OpMemberDecorate %FrameData 9 Offset 464
               OpMemberDecorate %FrameData 10 Offset 480
               OpMemberDecorate %FrameData 11 Offset 496
               OpMemberDecorate %FrameData 12 Offset 512
               OpMemberDecorate %FrameData 13 Offset 516
               OpMemberDecorate %FrameData 0 MatrixStride 16
               OpMemberDecorate %FrameData 1 MatrixStride 16
               OpMemberDecorate %FrameData 2 MatrixStride 16
               OpMemberDecorate %FrameData 3 MatrixStride 16
               OpMemberDecorate %FrameData 6 MatrixStride 16
               OpMemberDecorate %FrameData 7 MatrixStride 16
               OpMemberDecorate %FrameData 8 MatrixStride 16
               OpMemberDecorate %FrameData 0 RowMajor
               OpMemberDecorate %FrameData 1 RowMajor
               OpMemberDecorate %FrameData 2 RowMajor
               OpMemberDecorate %FrameData 3 RowMajor
               OpMemberDecorate %FrameData 6 RowMajor
               OpMemberDecorate %FrameData 7 RowMajor
               OpMemberDecorate %FrameData 8 RowMajor
               OpDecorate %frameData DescriptorSet 2
               OpDecorate %frameData Binding 3
               OpDecorate %frameData NonWritable
               OpDecorate %position Location 0
               OpDecorate %texCoord Location 1
               OpDecorate %normal Location 2
               OpDecorate %tangent Location 3
               OpDecorate %bitangent Location 4
               OpDecorate %gl_Position BuiltIn Position
               OpDecorate %worldPos Location 1
               OpDecorate %texCoord_0 Location 2
               OpDecorate %tangent_0 Location 3
               OpDecorate %bitangent_0 Location 4
               OpDecorate %normal_0 Location 5
       %void = OpTypeVoid
      %float = OpTypeFloat 32
    %v4float = OpTypeVector %float 4
%mat4v4float = OpTypeMatrix %v4float 4
    %v2float = OpTypeVector %float 2
    %v3float = OpTypeVector %float 3
%mat3v3float = OpTypeMatrix %v3float 3
       %uint = OpTypeInt 32 0
  %FrameData = OpTypeStruct %mat4v4float %mat4v4float %mat4v4float %mat4v4float %v2float %v3float %mat4v4float %mat3v3float %mat4v4float %v3float %v3float %v3float %uint %uint
%_ptr_StorageBuffer_FrameData = OpTypePointer StorageBuffer %FrameData
  %frameData = OpVariable %_ptr_StorageBuffer_FrameData StorageBuffer
        %int = OpTypeInt 32 1
%_ptr_StorageBuffer_mat4v4float = OpTypePointer StorageBuffer %mat4v4float
%_ptr_Input_v4float = OpTypePointer Input %v4float
%_ptr_Input_v3float = OpTypePointer Input %v3float
%_ptr_Input_v2float = OpTypePointer Input %v2float
%_ptr_Output_v4float = OpTypePointer Output %v4float
%_ptr_Output_v3float = OpTypePointer Output %v3float
%_ptr_Output_v2float = OpTypePointer Output %v2float
   %position = OpVariable %_ptr_Input_v4float Input
   %texCoord = OpVariable %_ptr_Input_v2float Input
     %normal = OpVariable %_ptr_Input_v3float Input
    %tangent = OpVariable %_ptr_Input_v3float Input
  %bitangent = OpVariable %_ptr_Input_v3float Input
%gl_Position = OpVariable %_ptr_Output_v4float Output
   %worldPos = OpVariable %_ptr_Output_v4float Output
 %texCoord_0 = OpVariable %_ptr_Output_v2float Output
  %tangent_0 = OpVariable %_ptr_Output_v3float Output
%bitangent_0 = OpVariable %_ptr_Output_v3float Output
   %normal_0 = OpVariable %_ptr_Output_v3float Output
         %33 = OpTypeFunction %void
      %int_8 = OpConstant %int 8
          %1 = OpFunction %void None %33
         %34 = OpLabel
               OpCopyMemory %texCoord_0 %texCoord
         %35 = OpLoad %v4float %position
         %36 = OpAccessChain %_ptr_StorageBuffer_mat4v4float %frameData %int_8
         %37 = OpLoad %mat4v4float %36
         %39 = OpMatrixTimesVector %v4float %37 %35
               OpStore %worldPos %39
               OpReturn
               OpFunctionEnd