I'm not sure i understand?
The better the system, the more revealing and transparent it is as well. The more it will expose errors of the source and reveal the true quality of the source. Better equipment makes it much easier to point out badly mastered pop CDs (I threw out half of mine when I upgraded) so why would it not be the same for an MP3 and FLAC?
Ok, let me try to make this a bit easier:
I agree FLAC is a lossless encoding.
I agree MP3 & MP4 are compression based encodings.
I agree that some torrent originated MP3 encodings are of substandard quality (blame the torrent and not the format)
What I don't agree with is that you can audibly distinguish any difference between an officially release MP3/MP4 and a FLAC encoded file. Equipment plays no part here (a better system does not make it any easier to hear differences). You simply cannot with any degree of certainty identify which one is FLAC vs MPX (we're of course ignoring those bad torrents, yes the one's we've all encountered at some point)
More to the point; an album purchased from iTunes (MP4) or Amazon (MP3) cannot be distinguished from a CD bought at Look & Listen (and of course encoded into FLAC).
FLAC then only serves as 'bragging rights'; mine is better than yours technically; but of course nothing we as humans can audibly distinguish.
So IMO to keep your music in a format like FLAC, a format which has so much accessibility limitations is all pain with no perceivable gain.
If you think I'm wrong; then show me a foolproof test we can conduct which will allow me and others to hear the 'difference'.