@sdexter – being new to DT myself, I don’t have anything to say about most of this, except on one point:
It seems like one point of friction here for an integrated workflow is that AFAIK Mendeley doesn’t offer much possibility of integrating with DT (or anything else). I have no experience with BookEnds, but I recently switched from Mendely to Zotero (b/c I didn’t like what seemed to me the increasing lock-in that Mendeley is pushing). I believe I was able to preserve all my tags.
And then, it appears that Zotero can be made to integrate with DT. Again, I have no experience with this, but here’s a thread that seems to suggest that Zotero+DTmay work about as well as BookEnds+DT:
If you are interested in looking more into Mendeley → Zotero, I can probably dig up some links and maybe some of my notes on the transition, if that would help. BTW I only ever annotated PDFs outside Mendely (and now Zotero) – if you’ve been annotating inside Mendely, I’m not sure how the Mendeley → Zotero migration wold go.