One library as a "master" library of files, many uncompressed / lossless, and another library that's a mirror for my portable devices with a lot of the same files, but in compressed, lossy formats.
Personally I do think maintaining 2 libraries a burden.
Why not using the synchronise option?
You create a playlist and sync this to the portable transcoding the format on the fly.
I found it easier this way to maintain a grip on how big the portable library would be, and to make sure everything is uniformly tagged.
I can see this becoming less of an issue down the line, so I might go the route you suggested eventually. After a couple of Bandcamp Fridays and Groupees bundles I started to run into storage issues on my DAPs and needed to pair down a lot of my lossless files, which resulted in me reorganizing my entire collection and the way I manage / organize my portable devices. And I think I had more control over things - ensuring uniform tagging, artworks, etc. - this way.
As to the issue itself, after making sure the "constantly monitor" folders stayed deactivated in the preferences, I have no longer had the libraries mix themselves into each other.
What I found interesting here was that it never happened to BOTH libraries, but only ever to one of them. But over re-building each of them a couple of times, it varied which of the two would get the other ones' contents inserted. So that's kind of an odd behavior...
I'll make loud noises should the issue still re-emerge, but it looks like it's been taken care of.
I guess it's a bit... Counter intuitive the way that you can have globally monitored folders and separate libraries that still include globally monitored folders - and then no good way of controlling the way individual libraries behave within MusicBee. Add to that the issue where you need to set "check at startup only" after unchecking constantly monitored folders in the preferences lest the folders just get reset to being monitored (if that makes sense) and... It's not optimal. But at least I think I now get where my problem came from.