This is true, but the DS9 coveralls were never intended or shown as being primarily for enlisted use -- and neither were the 'formal' TNG unis intended solely for officers.
And the result was that they weren't "primarily" used by anybody, and we are forced to accept that Starfleet intended them to be worn in a mixed manner.
But while the TOS movie coveralls had some offscreen intent behind them, this intent did not have any decisive onscreen result. It did not manage to establish that only enlisteds (and enlisted trainees, and perhaps cadets) could wear the coveralls, because how do you establish something like that? The audience might simply be failing to see those hundreds of officers who wear the thing, because they wear it outside the movies the audience sees and the camera records.
So the TOS movie intent really counts for nothing. Even ST2, which is supposed to introduce the whole uniform system, makes a mess of who is a cadet and who is not. Spock supposedly trains cadets, and Spock supposedly trains Saavik, but Saavik is never addressed as Cadet and wears the officer tunic with commissioned Lieutenant insignia. So, are the jumpsuit people the cadets? Peter Preston is addressed as Midshipman, but while wearing the (red-collared) heavy protective suit, and we never see him in a regular jumpsuit.