To put the fundamental problem simply, it is your approach that is "head canon", because it is in clear conflict with onscreen facts, that is, the Star Trek universe as portrayed to us. Errors are onscreen facts, therefore real.
But not always meaningful
, and therefore could be ignored as being either isolated cases or just minor breaches of protocol that nobody noticed. In the case of Valeris' shirt, for example, it actually works just as well to assume that the quartermaster simply ran out of red shirts in her size and gave her a white one instead.
And yet we see a large number of extras in the later TOS movies manning assorted stations on the various bridges. It could very well be that by the 2340s we see the outcome of a long slide towards greater complements of enlisted crew versus officers. Likewise, there are a good 20/+ years until TNG rolls out so that the reverse may have occurred (though with the Ent-D being the flagship by that point, this may not be par for the course throughout the fleet!) ETA: I assume of course you mean rank scheme, not uniform; since by that era the uniforms are... *ahem* uniform for all personnel.
Considering Chief O'Brien has effectively never been an officer throughout TNG, despite occasionally having the pips for it, it's entirely likely that a lot of the extras running around on the ship during TNG's run aren't actually officers at all. There may be some cosmetic difference in O'Brien's pips that doens't show up on screen; say, the officers pips are silver while the noncoms are bronze? The only thing indicating O'Brien might be an officer is when Riker calls him "Lieutenant" in that one episode; easily explained by saying Riker wasn't paying attention and misspoke.