That's specifically why I use mergerfs to avoid anything that.
I use merger fs with snapraid on my local dir since I have 24 x 6TB drives for storage there.
Would probably be messy to try and have a mergerfs mount of the remote and my already existing mergerfs which includes many things including my Movies folder 
Since I don't plan to have more things in "both" places I think the easiest way is to just dump a list of all the directories I have locally and rename all the remote ones that have the same name by appending something to the end.
My idea going forward is to have things I really want locally and other stuff, a series my kids want or something, downloaded and stored on the remote.
Not really, mergerfs is just a great tool for combining things.
You need some forethought on as I keep local and my rclone together in a single mount so my setup writes everything locally first and I upload at night.
A path never changes so Radarr/Sonarr/Plex/etc are none the wiser.
Having multiple paths for files is a management nightmare for those apps as none of them like things changing or going away.
Yea... But if they can handle a single movie having multiple versions (1080P and 4K or 3D) in different folder like
/Movies/Movie 1 (2010)
/Movies/Movie 1 (2010) [4K]
they should be able to handle it with
/Movies/Movie 1 (2010)
/Movies 4K/Movie 1 (2010)
and still keep track of which paths had been scanned. The old scanner seems to handle this better according to people who have run into this issue. So they must have made a bad decision during the design of the new one that is so tightly integrated into the entire thing now that it's hard to change.
Most people tackle that with different libraries.
With hardware acceleration and HDR tone mapping in the newer versions of Plex, I don't feel the need to keep multiple versions as I just let it transcode as it's almost no hit on my server.
For your specific use case and wanting to keep multiple versions for playback, mergerfs is not a good fit. When you first stated it, I read/thought you were talking about having a local and remote copy of the same file, which is a great fit for mergerfs and their policies.
Yea if one wanted all movies in both places that would be great. Can you "choose" to get locally existing files first and only play the remote one if no local version exists if you merge the local and remote folders together with mergerfs?
My mergerfs policy does a first found. I have my local disk first so everything goes there first and if not there, it comes from my rclone mount.
So that's exactly what I do.
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