That is normal. Emptying trash, cleaning bundles etc is for managing metadata etc within plex. Watched/Played status along with ratings are stored in a table which is not nuked by doing a plex dance.
I’ve not used MediaMonkey in years so cannot comment on that, I do use MusicBrainz Picard myself to tag all music within plex. I find this best as their tags play well with plex, especially for matching but other tools should work just fine if your tags are good.
Back to your original question, for the EP which is not grouping for you correctly can you show us what the releasetype tag has ? This is what plex uses for release groupings. I also assume you have Prefer local metadata enabled for your music library if you are using embedded tags.
