I agree with Till, the comfort of using my text editor to comment on my sources outweighs the benefits of Zotero’s magic (no need to edit the citation, which would mean about three extra clicks to do the same thing, and the ability to italicise or otherwise format my text; of course, on a Mac things like quoations marks are easier to get right to begin with, so it’s an easy trade-off).

At any rate, from what you’ve said, I conjecture that you’re willing to support both usage patterns, which is great. So it seems to boil down on whether, during the final editing process, it’s more work to capitalise those ibidems that should be capitalised but aren’t (because Zotero no longer capitalises ibidems after prefixes) or to lowercase those ibidems that should be lowercased but aren’t (because Zotero treats all periods as end of sentence).

And though that’s contrary to my own preferences, the latter seems to be somewhat easier, since it can be automated using a list of all abbreviations used (which will boil down to a single item, "cf.", in many cases) and simple search-and-replace patterns. By contrast, doing the former using search-and-replace patterns would seem to require some knowledge of regular expressions (or whatever their Word equivalent is).