Maybe that’s it? You’re looking for a difference and therefore you perceive one. I’ve not read the entire thread, but if you’re suggesting that each format leads to differences in the digital domain, then that’s bunkum, poppycock, tosh or whatever.
To prove the point, I converted some FLAC files to ALAC then to FLAC and back to ALAC again. Guess what? Each reproduces accurately and repeatably, i.e. they are all lossless and every file from each batch are identical.
Sound quality of AIFF, ALAC, FLAC and WAV is the same. The only difference is software/ hardware compatibility. So, if you are indeed hearing something it must be related to playback sound quality, i.e. the recording including mixing and post-production, the playback software or playback hardware.
But Roon is sending the DAC PCM, which is uncompressed, no matter what format you store your non-DSD music files in. The DAC has no idea what format the track was stored in. It could have been ALAC, WAV, AIFF, FLAC, or uncompressed FLAC. No matter what, the DAC gets the same PCM content. The DAC gets exactly the same bits in exactly the same order. So tell us, how does your DAC sound different if the data it receives is the same?
Are you connecting the Roon Core directly to the DAC or are you using a Roon Core and a Roon Endpoint?
EDIT: I saw in another thread that your compared uncompressed FLAC with AIFF and said AIFF sounded much better. Well, this problematic for your case as both uncompressed FLAC and AIFF have the same exact uncompressed data in them. There are some differences in the package the data is in between to the two formats but the differences are so minimal that the actual processing the system would do in either case would be impossible to differentiate. The file load time and CPU processing time required would be indistinguishable one from the other. In this case, it does not matter if you are using a Roon Core directly connected to the DAC or a Roon Core/Roon Endpoint setup.