.vscode\tasks.json

{
	// See https://go.microsoft.com/fwlink/?LinkId=733558
	// for the documentation about the tasks.json format
	"version": "2.0.0",
	"tasks": [

		// Papyrus Compile
		// --------------------------------------------
		{
			"label": "SkyrimSE Compile",
			"group": "build",
			"presentation": {
				"reveal": "always",
				"panel": "dedicated",
				"clear": true
			},
			"type": "shell",
			"command": "Tools\\VSCode\\Compile.bat",
			"options":
			{
				"cwd": "${config:papyrus.skyrimSpecialEdition.installPath}"
			},
			"args": [
				{
					"value": "${config:papyrus.skyrimSpecialEdition.installPath}",
					"quoting": "strong"
				},
				{
					"value": "CreationKitCustom.ini",
					"quoting": "strong"
				}
			],
			"problemMatcher": []
		},

		// Tools
		// --------------------------------------------
		{
			"label": "SkyrimSE: Start",
			"type": "process",
			"command": "${config:papyrus.skyrimSpecialEdition.installPath}\\SkyrimSE.exe",
			"problemMatcher": []
		},
		{
			"label": "SkyrimSE: Start (xSE)",
			"type": "process",
			"command": "${config:papyrus.skyrimSpecialEdition.installPath}\\skse64_loader.exe",
			"problemMatcher": []
		},
		{
			"label": "SkyrimSE: Creation Kit",
			"type": "process",
			"command": "${config:papyrus.skyrimSpecialEdition.installPath}\\CreationKit.exe",
			"problemMatcher": []
		},
		{
			"label": "SkyrimSE: Creation Kit Archive",
			"type": "process",
			"command": "${config:papyrus.skyrimSpecialEdition.installPath}\\Tools\\Archive\\Archive.exe",
			"problemMatcher": []
		},
		{
			"label": "SkyrimSE: xEdit",
			"type": "process",
			"command": "${config:papyrus.skyrimSpecialEdition.installPath}\\Tools\\xEdit\\SSEEdit.exe",
			"problemMatcher": []
		},
		{
			"label": "SkyrimSE: xEdit (64)",
			"type": "process",
			"command": "${config:papyrus.skyrimSpecialEdition.installPath}\\Tools\\xEdit\\SSEEdit64.exe",
			"problemMatcher": []
		},
	]
}

CreationKitCustom.ini

[General]
bAllowMultipleMasterLoads=1

[Papyrus]
sScriptSourceFolder = ".\Data\Scripts\Source\MyFolder"
sAdditionalImports = "$(source);.\Data\Scripts\Source\SKSE;.\Data\Scripts\Source\Base"

Directory Tree

E:\Games\Steam\steamapps\common\Skyrim Special Edition\Data\Scripts
\---Source
    +---Base
    +---MyFolder
    \---SKSE

Terminal Output

> Executing task in folder Skyrim Special Edition: Tools\VSCode\Compile.bat "E:\Games\Steam\steamapps\common\Skyrim Special Edition" "CreationKitCustom.ini" <

Compile.bat
----------------------------------------------------------------------
The data file to use.
FileName: CreationKitCustom.ini

The Creation Kit initialization file to use.
FilePath: E:\Games\Steam\steamapps\common\Skyrim Special Edition\CreationKitCustom.ini

The Papyrus Compiler executable to use.
PapyrusCompiler: E:\Games\Steam\steamapps\common\Skyrim Special Edition\Papyrus Compiler\PapyrusCompiler.exe

----------------------------------------------------------------------

Environment variable ImportResult not defined
SourceExtracted: .\Data\Scripts\Source\MyFolder
'""' is not recognized as an internal or external command,
operable program or batch file.
SourceResult: ""

ImportExtracted: $(source);.\Data\Scripts\Source\SKSE;.\Data\Scripts\Source\Base
The system cannot find the path specified.
ImportResult:


PapyrusCompiler: "E:\Games\Steam\steamapps\common\Skyrim Special Edition\Papyrus Compiler\PapyrusCompiler.exe"
SourceResult: ""
ImportResult: ""
output: "E:\Games\Steam\steamapps\common\Skyrim Special Edition\Scripts"
----------------------------------------------------------------------

Terminal will be reused by tasks, press any key to close it.

Tools\VSCode\Compile.bat

@ECHO OFF
ECHO %~nx0
ECHO ----------------------------------------------------------------------
SET Game=%~1
SET FileName=%~2
REM
ECHO The data file to use.
ECHO FileName: %FileName%
ECHO.
SET output="E:\Games\Steam\steamapps\common\Skyrim Special Edition\Scripts"


REM  ----------------------------------------------------------------------
ECHO The Creation Kit initialization file to use.
SET "FilePath=%Game%\%FileName%"
ECHO FilePath: %FilePath%
ECHO.
ECHO The Papyrus Compiler executable to use.
SET "PapyrusCompiler=%Game%\Papyrus Compiler\PapyrusCompiler.exe"
ECHO PapyrusCompiler: %PapyrusCompiler%
ECHO.
ECHO ----------------------------------------------------------------------
ECHO.
@SETLOCAL ENABLEEXTENSIONS
@SETLOCAL ENABLEDELAYEDEXPANSION
REM  ----------------------------------------------------------------------
SET SourceDepth=31
SET SourceResult=""
REM  ----------------------------------------------------------------------
SET ImportDepth=22
SET ImportResult
REM  ----------------------------------------------------------------------
FOR /F "usebackq tokens=*" %%A in ("%FilePath%") do (
	SET line=%%A

	@ECHO !line!|find "sScriptSourceFolder" >nul
	IF NOT ERRORLEVEL 1 (
		SET source=!line:~-%SourceDepth%!
		SET source=!source:^"=!
		ECHO SourceExtracted: !source!
		%SourceResult%="!source!"
		ECHO SourceResult: %SourceResult%
		ECHO.
	)

	@ECHO !line!|find "sAdditionalImports" >nul
	IF NOT ERRORLEVEL 1 (
		SET import=!line:~%ImportDepth%!
		SET import=!import:^"=!
		ECHO ImportExtracted: !import!
		%ImportResult% = "!import!"
		ECHO ImportResult: %ImportResult%
		ECHO.
	)
)

ENDLOCAL
ECHO.

ECHO PapyrusCompiler: "%PapyrusCompiler%"
ECHO SourceResult: "%SourceResult%"
ECHO ImportResult: "%ImportResult%"
ECHO output: %output%

REM "%PapyrusCompiler%" "%source%" -i="%import%" -o=%output% -f="TESV_Papyrus_Flags.flg" -all
ECHO ----------------------------------------------------------------------

These parts are extracting INI values but I fumbled getting the values into a scope I can pass to the compiler.

Source Extracted: .\Data\Scripts\Source\MyFolder
Import Extracted: $(source);.\Data\Scripts\Source\SKSE;.\Data\Scripts\Source\Base

I had trouble getting the extracted values into my the two variables.

SourceResult: ""
ImportResult: ""