The theory (and my practical listening experience) is, that flac is a compressed, lossless PCM format, while wav/aif is a non compressed lossless format. The renderer needs add. processing effort for flac while playing the file, which seems to be responsible for degraded sound.
There are different opinions on this and Ted points out that depending on care taken when comparing, various impacts could lead to differences so he sees this critically as you can read here:
https://forum.psaudio.com/t/firmware-versions-and-digital-sources/4630/14
IMO it’s easy to try if in your setup there’s a difference, so you can judge yourself. I tried it after an early recommendation of Paul shortly after I bought the DS, heard the difference and sticked to it.
If you hear it or not might be connected to the revealingness of your setup and/or the individual conditions within your setup or of your comparison.