The most valuable workflow is the one you have been using and happy with. I wouldn't wish a changed workflow on anyone in this state. I would only suggest another way for someone who is unhappy and already regularly changing. Stick with what works.
So maybe your use case does not match what a reference manager is for, but you also have not brought any informed criticism.
These aren't issues with any one piece of software, they're issues with coordination, as are the examples you mention.
Zotero is used primarily for managing the PDF library, the actual writing will happen in Word, LateX, etc. The reference list produced by Zotero is just text.
I don't see any real requirement that everyone working on a project would need to actually use Zotero, though I guess it would be handy to keep a coordinated shared library of papers.