Working version but slightly less parallel

CheckAllPairsSuccess.cs

using System.Linq;
using Unity.Burst;
using Unity.Collections;
using Unity.Entities;
using Unity.Jobs;
using Unity.Mathematics;
using Unity.Transforms;



[GenerateAuthoringComponent]
public struct MyThreshold : IComponentData
{
    public float threshold;
}


[GenerateAuthoringComponent]
public struct MyComponent : IComponentData
{
    public bool closeEnough;
}



public class CheckAllPairsSystem : SystemBase
{
    [BurstCompile]
    struct CheckAllPairsJob : IJobParallelFor
    {
        [DeallocateOnJobCompletion] public NativeArray<ArchetypeChunk> Chunks;
        [ReadOnly] public ArchetypeChunkComponentType<Translation> TranslationType;
        [ReadOnly] public ArchetypeChunkComponentType<MyThreshold> MyThresholdType;
        public ArchetypeChunkComponentType<MyComponent> MyComponentType;
        
        public void Execute(int jobIndex)
        {
            var chunk = Chunks[jobIndex];
            var translations = chunk.GetNativeArray(TranslationType);
            var mycomponents = chunk.GetNativeArray(MyComponentType);
            var mythresholds = chunk.GetNativeArray(MyThresholdType);

            var instanceCount = chunk.Count;
            ArchetypeChunk chunk2;
            NativeArray<Translation> translations2;
            int instanceCount2;    
            
            for (int i = 0; i < Chunks.Length; i++)
            {
                chunk2 = Chunks[i];
                translations2 = chunk2.GetNativeArray(TranslationType);
                instanceCount2 = chunk2.Count;

                for (int j = 0; j < instanceCount; j++)
                {
                    for (int k = 0; k < instanceCount2; k++)
                    {

                        // if checking against the same chunk, dont check against the same index,
                        // because that would be the same entity 
                        if (i == jobIndex && j == k) { continue; }

                        var a = mycomponents[j];
                        var aTheshold = mythresholds[j];
                        var aTrans = translations[j];
                        var bTrans = translations2[k];
                        var distance = math.distance(aTrans.Value, bTrans.Value);
                        a.closeEnough = a.closeEnough || distance < aTheshold.threshold;
                        mycomponents[j] = a;
                    }
                }
            }
        }
        
    }

    EntityQuery query;   

    protected override void OnCreate()
    {
        query = GetEntityQuery(typeof(MyComponent),
            ComponentType.ReadOnly<MyThreshold>(),
            ComponentType.ReadOnly<Translation>());
    }

    protected override void OnUpdate()
    {
        var translationType = GetArchetypeChunkComponentType<Translation>(true);
        var myComponentType =    GetArchetypeChunkComponentType<MyComponent>();
        var myThesholdType =    GetArchetypeChunkComponentType<MyThreshold>(true);
        var chunks = query.CreateArchetypeChunkArray(Allocator.TempJob);
        
        var checkAlignedJob = new CheckAllPairsJob()
        {
            Chunks = chunks,
            MyComponentType = myComponentType,
            MyThresholdType = myThesholdType,
            TranslationType = translationType
        };
        this.Dependency = checkAlignedJob.Schedule(chunks.Length,32, this.Dependency);
    }
}