So I just saw that the Plex now lets you choose aired vs dvd order on a series basis without having to switch to another agent (TheTVDBdvdorder), which is great and I somehow totally missed this new feature. Unfortunately the thumbnails are still those of the aired episodes rather than the correctly named episodes.
Example Firefly: episode 1 “Serenity” is correctly named but the thumbnail is from “The Train Job” as it is episode 1 in the aired order.
Tried rematching and refetching metadata couple of times, but it keeps showing the wrong thumbnails.
Currently using 1.6.1.3722-4955e31cf on Synology DSM 6.1.1-15101 Update 2.