That name style should work. Plex REALLY only cares about the “SxxExx” numbers and ignores pretty much anything else about the file names. I leave out the show name in my files, so “S01E01 - Pilot.mkv” works, but so does “S01E01.mkv”. Plex doesn NOT take into account any info in the file name past the “SxxExx” part of the filename (for the most part. Plex does look after this if you have episode-specific featurettes or split episodes, but those are rare to me).
I’d like to know if you are doing the Plex Dance for these files whenever you rename them? Doing an in-place rename will not work. Copy the files out of where Plex is watching, scan the library, rename the files, add the files back, scan again.
Edit: Looking at TMDB vs TVDB, ifyou have a lot of DVD specials or alternate Pilot episodes, I’d suggest you set this show to TMDB (Aired), rather than TVDB. I like TVDB normally, but I’m shocked at how few specials it has compared to TMDB.