To update on my previous post, most of the issues listed have been fixed in the latest version of Scrivener, by removing some of the overrides it was using to fix other problems in the spell check engine, and making it operate pretty much vanilla in terms of how it works with most other software.
The “Learn word” issue does sporadically remain, though at this point there isn’t anything more we can do about it, and will have to hope that its reliability is improved in future versions of macOS.