C# array within a struct

Use fixed size buffers:

[StructLayout(LayoutKind.Explicit)]
unsafe struct headerUnion                  // 2048 bytes in header
{
    [FieldOffset(0)]
    public fixed byte headerBytes[2048];      
    [FieldOffset(0)]
    public headerLayout header; 
}

Alternativ you can just use the struct and read it with the following extension method:

private static T ReadStruct<T>(this BinaryReader reader)
        where T : struct
{
    Byte[] buffer = new Byte[Marshal.SizeOf(typeof(T))];
    reader.Read(buffer, 0, buffer.Length);
    GCHandle handle = default(GCHandle);
    try
    {
        handle = GCHandle.Alloc(buffer, GCHandleType.Pinned);
        return (T)Marshal.PtrToStructure(handle.AddrOfPinnedObject(), typeof(T));
    }
    finally
    {
        if (handle.IsAllocated) 
            handle.Free();
    }
}