The one thing I wish Zotero would have is the ability to export (and then version control) the collections layout. I don't really trust Zotero to not at some point mess this up, especially if I'm trying to sync multiple accounts after an internet outage, and having the collections layout backed up would really make me trust the platform a lot more.

Yeah, Zotero w/ Better BibTeX is what I use for all of my papers/bibliography. It also keeps .bib files updated as you add stuff to the bib database. This lets you write your paper and add references to the database without worrying about exporting the file over and over again.

It's so good that I don't even think about my bibliography anymore, except when correcting non-standard author name silliness (weird and wrong punctuation and other stuff that happens when pulling nonstandard DOI entries).

Jep Zotero is where it is at! The bibtex support is also very good. So you can do your papers in word an still have a nice latex thesis later.