versions show as separate titles for some movies

[Efficient_Good_5784]

Try removing (2002) from the FILE name.  It is fine to have it in the folder name.  If that doesn't work, its possible that the fact that they are in different containers is problematic.  The docs don't say anything about extensions, but I wouldn't be surprised if "versions" needs them to be in the same container.

Remuxing should only take a few minutes.

The Docs specifically say that the file name should match the folder name exactly, followed by any labels. "The prefix has to be an exact match of the folder name for the versioning to work, " as seen here https://jellyfin.org/docs/general/server/media/movies/.

Also, whether the extensions are the same or not does not seem to matter. As shown in my original post, the bourne identity is successfully identified as different versions instead of different listings despite having different extensions. There are other movies where the versioning works just fine with different file extensions. As well as movies where versioning works fine with movies with the same extension.

Did you try @TheDreadPirate's advice to see if it worked or not?