Thrilled to have most of my MakeMKV workflow down. Rip video, rip the top DTS-MA audio (not sure why it always defaults to the 5.1 track). Usually rip and DD tracks (commentary usually). And English sub tracks. Video is usually encoded to H264 these days, so as long as the Apple TV is on my 5Ghz network I can select 40Mbps and get native video playback (no transcoding). Hoping that Plex adds transcoding to eac3 soon. I tried modifying the tvos.xml file on my Mac but it must have broken the .app bundle because plex stopped working.......
Been a while since I've done iOS development, but if I remember, yes your ROMs will be fine. It only overwrites files and binaries as part of the source code. So any saved/generated files from the app don't get blown away unless you delete the app.
Regarding 3, not from the tvOS UI that I've seen.
Regarding 2, if you mean from the web interface to Provenance, yes. If you delete it from that "web page" you are deleting it from the Provenance sandbox (file system).
I suggest you read those guidelines. Netfix, Hulu and even HBO (which is a substantial redesign) all adhere to the tvml templates. It doesn't fall at all at Apple's feet. Even more than that.... Sadly there are reasons Netflix for example is worse. The old UI was very much about giving you direct control over what you found and watched. Netflix really doesn't want that. They would much rather your watch what they push and promote. They pay a lot of money for that stuff and want to get value from it. This is why your list is the very last entry on the UI (usually 30+ rows down). It has nothing to do with Apple and everything to do with Netflix. Same thing with Hulu. Both UIs are worse, and it all comes down to marketing what they want you to watch. However, both apps are WELL WITHIN Apple's interface best practices and all use the standard tvml templates.