This is an excellent analysis. And you are totally right about Chakotay: he is never ever referred to as "Lieutenant Commander". I like your Watsonian explanation! That's a really interesting take.

Of course, this is also the show that was bizarrely inconsistent with Tuvok's rank. Interestingly, between Kes, Neelix, the Doctor, and Seven, I think VGR may have had the most rankless characters of any series up to that point. I suppose DS9 could be tied, since VGR only had three rankless characters at once, as did DS9 (Quark, Odo, Jake).

But yeah -- I wonder if this reflects a larger trend. ENT definitely leaned on simplified ranks as well -- instead of the TNG-era 7-rank scale, we only ever see four on ENT: Captain, Commander, Lieutenant, and Ensign. (It's not clear to me that the costume department even designed a "hollow pip" for the ENT uniforms.) Under that analysis, we see a gradual trend toward de-emphasizing rank, from DS9 to VGR to ENT to DSC to PIC & PRO (though not LDS).