First, I am in no way a developer or programmer. I know just enough to be dangerous. 🙂
I recently did as you described and imported eXoWin3x alongside my existing eXoDOS inside LB. I followed the eXoDOS directions but did not copy over anything in the eXo folder except the eXoWin3x folder, leaving the original eXoDos copies of the dosbox, mt32, and SHADERS folders. I also left the original plugin file in the plugin folder.
Worked great.
Now to save space like I do with eXoDOS, I did not copy all the game .zip files over. I don't have the 340+gigs of free space (just like I don't have the 560+gig free space for the eXoDOS games). However, unlike eXoDOS, eXoWin3x does not have the download capability so I just plug in a smaller 500gig external drive I have devoted to Win3x and just copy the games over when I intend to play them. Tedious I know but them's the sacrifices we make.
Anyhoo, I wanted to still have a playlist similar to Installed eXoDOS Games, but the setup did not include an .xml for eXoWin3x, I assume since it just assumed the .zip files are all in place, present, and accounted for (even if they haven't been extracted yet).
I noticed that the metadata for the exoDOS games had the Installed toggle with a white square box (I'm sure there's a more precise naming convention for it) but once the game is installed (.zip extracted to the appropriate folder) then the metadata was changed to a check mark, therefor appearing on the installed playlist.
For eXoWin3x, all the titles also just show the white square, but that toggle DOESN'T change after installing it (double clicking and going through the setup process).
I even copied the existing Installed eXoDOS Games .xml file to a new one, made changes so it would look in platform Windows 3x, and even changed the playlistid (I read they need to be unique, but not sure how dangerous it is to just make up a number) and it worked once. After that not again.
So that's where I stand. Hopefully someone much, much, much smarter than me (you know, a normal person) can come up with a real Installed eXoWin3x Games .xml and/or a way to have the games automatically toggle the game metadata to a check mark when the .zip is extracted.
Sorry for the long drawn out answer to your question.
TLDR: yes they work together.