It’s funny, I have been following this thread and was appreciating the interesting discussion. I’ve never really thought much about the inherent dissonance built into a M7 chord, probably because it just sounds so “beautiful” and perfect.
However, one song I’m currently writing has a couple of M7’s in it. Playing it unplugged on guitar everything sounded fine, but once I plugged it in, I was hearing something “not quite right” in the verse. Just us the OP described, it was actually the root in the bass that sounded slightly out of tune, if I had to pick a note/string. This conversation popped up in my head, and I checked what was happening with the melody. Toggling to a M6 for that part of the verse, kind of a common move, made everything “right” again.
Pretty fascinating, as that root note can’t really be “out” in any logical sense. But I believe it is the root vs. M7th dissonance being highlighted against that particular melodic passage.