Not that this helps with your problem, but I thought I would explain a little about the 2 keys. You have 2 keys because there is a separate key file for plus and pro. When you upgraded to pro the plus key wasn't deleted, and that is probably a good thing. Why delete something without warning and take the risk that something didn't go quite right.
And FCP warns when you have multiple keys because if you ever need to get a new key for a new flash, it could happen that the wrong key gets replaced. Not sure whether that could really happen with different levels of keys (plus,pro), but probably that hasn't been tested.
You can delete the unneeded key yourself. It is on the flash drive in the config folder.
Extremely unlikely any of this has anything at all to do with your plex issue. The docker and plex don't know anything about the keys.