A sonic preference for one lossless type over another lossless type can be readily explained by neurophysiology. Millions of hair cells are tuned to specific sound frequencies inside our ears. The sensitivity of these cells to becoming excited by their tuned freqs will vary with age: many actually die off with age (and with usage: louder music will kill off cells, leading to hearing loss). A perceptual difference between WAV/FLAC/AIFF is explained by the responses of the remaining hair cells to identical freqs of sound waves. To further complicate things, all cells are plastic -- they respond in a variable manner depending on prior experience (i.e. history of listening). Some hair cells also become stiffer with age or with chemical damage, making them harder to excite at specific freqs. (Taking certain antibiotics for a long period will kill inner ear cells, leading to partial hearing loss).
A few other variables also come into play, such as head position/angle and emotional mood when comparing file types on a system.
In the end, a lot of things can happen before the sound waves reach my brain to allow me to perceive a music file as sounding the "same" or "different".
None of the above, as far as I understand your argument, has anything
to do with the file type per se- your hair cells, whether healthy or not, do not change characteristics when you are playing a FLAC file (which, to repeat myself, unpacks into a bit-perfect replica of the original file) vs, say, an AIFF or WAV file. Neither do the file characteristics change when the angle of your head (or your state of mind, or attentiveness), change- although any of these things can affect our experience
of a musical event, they have nothing to do with the characteristics of the file itself. I might be more relaxed on one occasion and my system 'sounds better' and bothered by something another time- when I was a younger person, my stereo used to sound better after some herbal 'enhancement' even though I know that the sound of my system didn't actually change, just my perception
thereof- but those are not inherent SQ issues, which as I understand it is the original topic.