If the UFP Starfleet's ranks were distinct, that would be one thing. But they're (at least for the officer ranks) identical to US Navy ranks. I don't see any reason to assume there was a "zig-zag" in the lineage instead of just letting that straight line go through.
You're forgetting that there was no lieutenant junior grade rank in TOS -- it went straight from ensign to lieutenant. And commodore was evidently phased out sometime in the movie era. So there's already precedent for Starfleet changing its rank structures over time.
I'm not convinced it was conscious. I don't recall (nor has anybody posted in the thread that I noticed) any proof from the show that there those ranks didn't exist.
They designed four pins for four ranks. Design reveals intention. If they'd wanted there to be a lieutenant commander's rank, they would've designed a rank pin system that included it, that would've had some recognizable gap to allow for it even if it wasn't seen. And surely it would've been seen somewhere in the course of 98 episodes, even if just on a background extra.
And "no proof it didn't exist" is a nonsensical argument when talking about a fictional series. If you postulate the existence of something beyond the canon, that's something new that you are making up and adding to the fiction, like I do when I make up a new character or a new alien world. And such a creation ought to serve a purpose. I see no reason to add this particular idea to the fiction, especially when it clashes with the insignia design. It's a poor fit. And I don't see what benefit there is to it, what you gain by having it, other than conformity to what other Trek series have done, and where's the value in conformity?