The result from the following command is different on Windows compared to that on macOS and Linux.
bin/basisu -hdr_6x6i -hdr_6x6i_level 12 -output_file R16G16B16_SFLOAT_2D_8x8_LEVEL_12.ktx2 R16G16B16_SFLOAT_2D_8x8.exr
This is the source file: R16G16B16_SFLOAT_2D_8x8.exr.zip
For levels 1 to 11, the result is identical on all 3 OSes. I used GCC 11 on Linux, Clang 17 on macOS and CLangCL 19.1.5 on Windows. The compiler does not seem to matter though. The same result happens with ClangCL or MSVC (19.44.35222).
The largest pixel difference compared to the Linux/macOS result is 612.0 (compared after transcoding to HALF). As a percentage of the smaller of the 2 pixel values that is only 2.2% not nothing major. The input image is a stress tester from our test suite, so an edge case. With a, perhaps, more normal input, Desk.exr that you have been using, both level 11 and level 12 show similar to each other, and much smaller compared to the 8x8 case, differences from the macOS generated images. I haven't tried to compare the Linux generated output in this case.