I think you are on to something. However, one of the things I have done is I have created a completely different directory for TV Shows Mislabled By Plex already - as the Split Apart option doesn’t even show up half the time. I use this for when there is an alternative version of a show (for example, Star Trek TOS original special effects vs remastered, Red Dwarf Original vs Remastered, or when a show reairs and there is an extended version or if it airs with tweets and facts that were not in the original version).
So this has worked well so far.
So I think I am going to have an additional folder for television Bonus features. This parent folder will be TV Shows, and then I will use the local media agent on it, then just supply my own series pics. This is messy but it should work.
As for the naming of Doctor Who Bonus Features, you have Bonus Features to the specials, which is what gave me this idea. So, this should work with your directory naming
So, The Five Doctors is episode 2 in season 0, and there are 106 specials listed on thetvdb
So, when scrolling my libraries on Plex, I have
TV Shows
TV Shows - 4k
TV Shows - Alternative Versions
TV Shows - Animated
TV Shows - Bonus Features
TV Shows - Mislabled By Plex
So under TV Shows - Bonus Features
\Doctor Who (1963)
\Season 00
\Doctor Who - s00e00201 - The Five Doctors - Celebration.mkv
\Doctor Who - s00e00202 - The Five Doctors - Trails and Continuity.mkv
\Doctor Who - s00e00203 - The Five Doctors - Photo Gallery.mkv
And so forth. Plex should then not try to match them with any Database since I am using Local Media Agent, but should still split it apart by show and season, and then underneath the season should display them in order.
Episode numbering is exxxyy where xxx would be the real episode number the episode corresponds with, and yy is just numbering of the bonus features on the disc.
The downside to this is that your Bonus Features won’t be with the show itself, but the upside is it makes it easy to organize and keeps Plex from trying to group your bonus features as alternative versions of your show.
EDIT - I thought Plex pulled the episode name from the file name, but it looks like it doesn’t. You will have to edit the episode name by hand in Plex. Not a huge issue - this works, just an additional step. Still, this worked brilliantly.
EDIT 2 - AND, something is not working right. Dropped Several more bonus features, and it is still only showing 4 after a rescan, although it changed the episode number of that last one. I moved the directory, rescanned, put it back, rescanned, same issue. Completely deleted the library, upgraded Plex server, recreated the library, scanned, and still 4 episodes. It seems that Plex has a maximum episode limit. Looks like a workaround is going to have to be to list the file names sequentially, import them into Plex, label them, and then use the Sort Title option
EDIT 3: Eureka! The issue was that the extras I dropped had -featurette, -interview, -deleted at the end of the name. It looks like the TV Show agent will just completely ignore those files (I think someone mentioned that earlier. Now that I got it all working, I need to go back and rename the shows and the add the artwork, but hey, its working, and I can keep my episode numbers! So ignore my second edit.