If you can live with typing/pasting in all meta data manually, sure.
No, Plex will use the guid="xxxxxxx"
identifier to distinguish items. You can see it by looking at the Plex XML info of your library items.
They should not, unless they are matched to the Personal Media agent.
Have you tried to remove all versions of this movie during a Plex Dance (no matter whether they reside in different libraries or not.)
Afterwards, add temporarily only one of the versions back and see if the chapter markers are correct.
Have you played the file in e.g. VLC, to see whether the embedded chapter markers are correct at all?
Have you checked the MKV files with MKVtoolnixGUI to see whether they may contain several different versions of chapter markers?