Never worked with Zotero, just with Bookends. So, I can say what I love BE for:
- Deep integration with Mellel (powerful word processor for manuscripts, with live bibliography)
- Wide AppleScript support
- Very flexible formats manager
I import all articles in DT and connect them with corresponding refs in BE. Script does it all in one click. Another smart rule is run on a timely basis to sync them if there are any changes from both sides.
The purpose of importing over indexing is not just search and stability - it is organizing power of DT: groups, tags, reps, annotations and etc. Many of it is impossible or may brake if you rely on indexing.