I find that very short-sighted. As soon as your plex server craps out, you’ll lose all your metadata edits. If those metadata are stored directly in the media files, you can easily rebuild your plex data base.
And if you happen to use other media players as well, those can benefit as well from the embedded metadata.
@themdg this might be of interest: What MP4 tags can be read into Plex with local assets agent? - #9 by kwarner04