So, you know how BioShock Infinite does that extremely jarring thing of applying the typical lib anticommunist "both sides suck" thought terminating cliché to a slave revolt? That's probably a product of rewrites.
In early interviews, Ken Levine talks about the Vox as "starting as kind of a student movement, working to unionize workers, protect rights of minorities" and an "internationalist movement, a worker's movement". IIRC there's even some vestigial elements of that in the final game, like the red color scheme, and an audio log that unsubtly draws a parallel between the Vox and the khmer rouge, something about going after people with glasses/intellectuals (I might be missremembering this last one, since I couldn't find it by CTRL + F on a transcript).
There were so many rewrites on Bioshock Infinite I'm certain the final script wasn't in place until maybe 9 months before release, despite 6 years of development. The 2012 E3 demo shows scenes that didn't make the game, like main villain Comstock has a completely different role. These scenes weren't simply little basic dialogues or small levels, they were entire scripted sequences with full Troy Baker voice acting and setpieces. Comstock was a lot younger in earlier demos, Fitzroy had a Caribbean accent, and the Vox Populi was more fleshed out.
The final game feels messy, like a patchwork quilt of a hundred different smaller ideas. Like you said, vestigial elements. The entire game feels like a vestigial element of various unformed thoughts Ken Levine had, except he was probably given too much money and had too high of a reputation after Bioshock 1 for 2K to say no. Pretty sure that's why Levine's latest project has such high turnover and it's been close to 10 years now. He has infinite money from 2K.
It's a shame because I really like Bioshock Infinite. I really like old timey 1910s settings with handlebar mustaches and malt shops, and at least Infinite is bold enough to show the setting is implicitly racist. There is a surprising level of criticism against American imperialism, something you didn't see much from big budget games, especially not an FPS. Except the plot screws up by portraying a rebellion against racism as bad or worse than the society perpetrating it.
That's apparently just how all Levine projects go:
From this article (or archived here). Typically you wouldn't see having to do massive crunch at the end of development as somehow a positive, but the genius auteur mind of Ken Levine understands that being forced to rush things right at the end is good for art actually.
This is what Mensa brain savant Ken Levine calls "environmental storytelling"—simply make your company a hostile hellhole to work for, and the story gets done.