Hi Charles, thanks for the detailed answer. Based on it, I think I can go on syncing multiple devices with multiple libraries without issues. My setup: All Calibre libraries are under a single installation, I do not use plugboards, and all books across the multiple libraries each have a unique title, even if they are the same literary work.
I think the logic in CC is well thought out -- and safe, at least for the way I use it -- and I have peace of mind knowing I will not end up with a jumbled mess one day.
BTW, initial syncs with 1.13 were of normal length for my setup and didn't take a long time like it has in the past.
--Pat