JuiceWSA, thanks for the response. Forgive my assumption if it’s wrong, but I think we might be kindred spirits in as much as we both seem to put a lot of effort and time into something which, arguably, is not very important. 
Your reply and linked post reminds me of some of mine on a support forum for an old favorite browser of mine. Because of that, I’m going into a little more detail than I normally would. I sometimes wish I had more time for troubleshooting and experimentation these days.
My problem is solved, and I think I know why I was getting the result I was getting… and I also don’t think I really did have a problem in the first place. But, while I don’t doubt your system works and maybe gets someone where they want to be faster, from this experience, it doesn’t seem to be necessary. Plex, though, is definitely behaving differently than it did in the past, so I’m a little curious as to when things changed.
I did a quick scan and have a little over 20 movies in my library that have different versions. I’m pretty sure I haven’t added any since your 2019 post. That naming method I described in my first post is how I’ve done it for awhile, but I followed every step you gave (except one!) and ended up with the same result. For some reason I don’t recall, a week or two ago, I was in my Agents section of my settings and was playing around with the order (I think The Movie Database combined episodes where TVDB didn’t, or something like that). Because of that, I “knew” Local Media Assets were at the bottom of all of my Agent lists… which it turns out, they weren’t.
I should add that while I was doing all of this re-naming and moving, I was actually in the middle of 15 other things, so my attention was never 100% on it. So, while I thought I was getting consistent results adding stuff back to my library, I think I was really just catching Plex on the figurative ‘Step 2’ sometimes and ‘Step 5’ at other times.
Once I thought I wasn’t getting a good result with your naming method, I went back to mine. Now, everything is back the way it was. Off the top of my head, the only time I know I’ve added Special Features to a movie in which I already had multiple versions is with the Alien movies. I had all 4 and then bought the set with the Director’s cuts. The originals were already there and I added the new versions with their special features. I would have added the movies first, though, and let Plex find them because that’s how I always do it. I then would have split the movies and after that added the special features. I didn’t have any issues doing it that way.
It seems like a large part of the ‘problem’ I posted about was that, I’m guessing one of the server updates, had moved Local Media Assets up to the top of all of my library agents. Before all of this, all of my special features had been fine, but once I did that initial rename, Plex was throwing them all into my main Movie library as other movies. It didn’t really click for me what was going on until I recreated my special features folders and accidentally named the ‘Other’ folder ‘Others.’ The only thing in that folder is the fan cut causing all of the problems. This time, however, instead of bring it up as “The Other Woman,” Plex brought it up as “The Others.” That’s when I realized I needed to actually go in a double-check the agents and saw LMA was at now at the top.
When I went back out, Plex was showing the trash can over top of the “The Others” poster. Clearing trash made the movie go away, but obviously, left it in Superman’s special features. Problem solved. (And thinking back, I realize that I did actually run into that before, but since I was doing other things, I only tried having Plex delete the movie and completely forgot to try emptying the trash.) For the sake of experimentation this morning, though, I left Local Media Assets as the first agent in all of my libraries… but this time, I let Plex sit while I added stuff back.
So, I had already scanned the library, emptied trash, and cleaned bundles. At this point, all I had done was add Superman.mkv and the Others folder containing the fan made cut back to Drive:\Movies\Superman\Superman (Theatrical Edition). I’ve always kept my special features in folders, so I added my Behind the Scenes folder, and went and got my breakfast. When I came back, the Behind the Scenes files were on my home page, but had the trash can on their covers (which hadn’t been matched to anything/were just showing screenshots) and were being removed with no action from me. I came back as they were disappearing. So, then I added the Deleted Scenes folder (which had 4 more files, but were all shorter and smaller in size and length). For some reason, it took about 20 minutes for those to all start showing the trash can and, this time, I had to empty trash manually. When I added my Scenes folder, I had to manually scan and manually empty trash.
For testing’s sake, instead of adding my last folder (Trailers), I went ahead and added the other two versions of the movie. No matching was necessary for any, but obviously, I did have to split them. Then, I added my Trailers folder and everything is back to normal. The three Trailers files didn’t show up on my Home page at all. (Maybe because there were only three and they are tiny?)
So, going back to my original post… I think my issue was clearly caused by the Local Media Assets being the first entry in my library Agents. However, I think I wasn’t giving Plex time to do its thing. I saw it pop up as a movie and took action before Plex decided the new ‘movie’ was unavailable. I’ve come to realize that I’ll admit that I have a total of 8 versions of Superman thru Superman Returns, but the thought of having a Cameron Diaz movie in my library makes me drop everything and immediately get to work on getting it out of there. 
Do you think Plex creating entries in my main library is caused by my LMA agent priority? That makes sense to me, but it’s weird that, for all of the talk about file naming and folder structure, it’s creating “The Other Woman” entry out of “M:\Movies\Superman\Superman (Theatrical Edition)\Other\ ‘The Final Cut’ Fan Made Remaster.mkv”. I get where it’s pulling the 'Other" but geez. As I said, though, everything is back to normal… the Special Features are in their own folders in my ‘Theatrical Edition’ folder and they’re showing for all versions of the movie in Plex. If anyone is having problems, my guess is that it’s more related to not scanning, emptying trash, and cleaning bundles than anything.
On a related note, I do know at some point, it didn’t matter in what folder the special features were. I initially had all of my special features in the ‘alternate’ version’s folder. But when I decided to split them based off of what version to which they related (I think with E.T.), they all showed up under each movie anywhere, which frustrated me at the time. Clearly, something about how Plex deals with this has changed and, again, I’m not sure when that was, but it was a while ago. I decided then, though, that if they were all going to be together, it made more sense to put them with the original movie and all I did back then was move them and rescan metadata. I think there probably were some I had to remove and add, but I know I didn’t have to do that with the majority. Also, regarding when Plex’s behavior changed, I’m pretty sure it wasn’t like this in October 2018. Oddly enough, it’s related to Superman again, but that’s around the time I bought the Extended Edition. A week or so later, they released the 4K disc and I bought that. So, it’s at that time that I would have added the Extended Cut folder and had no troubles. I don’t think any special features were added at that time, but they did appear in the Extended Cut in Plex.
Wow… that’s long. It looks, though, like you’re the person for this, so I wanted to get down as much knowledge of my experience as possible. I’ll end this here and now go change my library agents before I forget. Thanks for your help, input, and previously typing up information regarding this.
