Plex supports different (quality) versions of the same video. This is not designed for different cuts / editions.
There’s a very popular feature suggestion with tons of ideas on how to handle this – though no confirmation if this will ever be implemented (or how).
#2 will depend on your file naming. Plex doesn’t deal with / support a general extras folder. With proper naming, the files should show up properly as extras of that particular movie. You’ll need to share the exact folder organization and file names for further feedback
https://support.plex.tv/articles/local-files-for-trailers-and-extras/
