Idk, on Kodi I had to rename my files a certain way for them to be associated with metadata from IMDB & all, so I was used to having Filebot[1] doing the job for me. When I switched to Plex, I didn't even think about it, I kept renaming my files with Filebot. Also I prefer the light and clearer pattern that is resulting from Filebot instead of having weird filenames depending on the release.
[1] : https://www.filebot.net/
I would like to be able to just point to a file and tell Plex what that file is so it "knows" (puts it in it's database). If it can read/write metadata on the file itself, that would be great too.
That's like arguing that they prefer an unsorted pile of thousands of books vs. a library/bookstore. I mean if that's how they want it then fine, but you don't get the useful features.
There are a multitude of metadata managers out there which don't require the same directory structure but they are a load more effort than automatic metadata matching and a lot more effort than simply organizing your media in the first place.
Your solution works for MKV files. The Plex solution works for all file types and containers.
It's easy to see why Plex would prefer this way.
It has an edit button in the UI for entering in the metadata to its database manually.
It has the option to prefer metadata already stored locally inside the container when populating its database.
It has the "match" button for interactively discovering and retrieving the metadata from an agent like IMDb or tvdb regardless of filename.
By default it tries to spare you having to do any of these things, but they put a lot of work into facilitating several alternatives when you'd rather do the work yourself.
For whatever bizarre reason, Plex all but requires you conform to specific filename formats. I don't why, but this pisses me off to no end.
What's the point of having elaborate media containers like MKV if you can't just point to an arbitrarily named file, process, fill-in, or read the metadata and have it added to your library? I mean, Plex maintains a database, can read metadata, pull info from moviedb, tag stuff, categorize... what's up with the obsession on filenames?