Replace the bundle that comes with Plex with this one. On linux, that's:
/usr/lib/plexmediaserver/Resources/Plug-ins-xxxxxxx/TheTVDB.bundle
where xxxxxxx is the short-rev Plex appends to the end of their version strings. You need to check out the feature/dvd-order branch (git checkout feature/dvd-order); the default branch (latest; the one that gets checked out automatically when you git clone) is just the code for the most recently shipped version of the agent (the plexinc-agents/TheTVDB.bundle repository isn't up to date with production code). I update both branches automatically when installing a new version.
No need to switch agents for the shows that need DVD ordering. Go to
Settings -> Server -> Agents -> Shows -> TheTVDB
and click the gear next to the TheTVDB line to open the agent options. There's a new field to enter a comma-separated list of TVDB series ID numbers to use DVD ordering for. For example if you have Firefly, and S01E01 in your folder is "Serenity" and not "The Train Job", put 78874 in the field and then re-match the series ("fix incorrect match").
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