The Play Version capability is not meant to differentiate between Director’s Cut, Extended Version, etc. It shows if the files have different resolutions, to assist with choosing the right version for a mobile phone, SD vs HD, etc. See the Multiple Versions of the Same Movie section of Multi-Version Movies.
The best way I’ve seen to do this is to keep each version in a separate folder, as if it is a separate movie. Plex will still combine them, then you manually split them apart. Ugly, but it works.
Something like this:
/Movie (year) [theatrical]/Movie (year) [theatrical].ext
/Movie (year) [director_cut]/Movie (year) [director_cut].ext
Regarding the square brackets and metadata matching…
Plex just re-wrote the movie agent from the ground up, starting with the PMS 1.20 releases.
It would be nice for somebody from Plex (Ninja, Team Member, Employee, etc) to provide details on how the new agent responds to square brackets.
As noted in the support article you linked, starting with the 1.20.1 releases you can add the IMDB or TheMovieDB id to the folder & file names. Plex will use this info to match the movie, so how Plex responds to square brackets may be moot.
FWIW, even with the prior agent, now called “Plex Movie (Legacy)”, I do not remember the square bracket behavior being formally documented in the support articles.