Collections in 2 movie libraries

I believe there might be some confusion.
If you create a new library (or update an existing) one to the new Plex Movie scanner/agent, Plex will indeed automatically create collections. You can set a threshold for the minimum amount of movies of a collection you want to have before Plex creates a collection entry.
While The Movie Database agent basically just tags the movies (if configured to automatically get collection information from The Movie Database), the new Plex Movie agent will also get posters, backdrops and the description.

There’s however a caveat when it comes to updating an existing library.
When updating your library from the legacy Plex Movie agent, Plex will not overwrite manually populated collection tags. If you want Plex to create those collections automatically with that agent, you might need to delete/clear existing collection tags and ensure their collection tag isn’t locked.

From https://support.plex.tv/articles/201273953-collections/#toc-6

Where did all these extra collections come from? I didn’t add them.

There are three ways “automatic” collections can be made.

  1. You may have enabled the Use collection info from The Movie Database metadata agent setting. When enabled (it is disabled by default), that will try to gather collection information from The Movie Database. This may cause many unwanted collections to be automatically created, particularly collections where you only have one item. You can disable that preference in the server metadata agent settings for the “Plex Movie” and “The Movie Database” metadata agents. This will only prevent collections from getting automatically added to items added to your library in the future . It will not remove collections from existing library items.
  2. If you are using Plex Media Server 1.20 or above and are using the Plex Movie agent you can set how many items minimum to create a collection. You can set it to Disabled if you do not want it to automatically create collections.
  3. If you have MP4s with an embedded “Album” tag, the Local Media Assets agent may pick it up as a collection. Be aware the Local Media agent also picks up external subtitles, extras, and other embedded metadata in MP4s (and other files), so be aware of this if you choose to disable the agent source.