It is actually just one database. Which is fed by several sources for metadata. TMDB is used as the primary source.
Those different episode ordering options are just additional properties of the main item. So if you use the TVDB ID during matching, it will still match your item against the main list of media (which is supposed to hold all tv shows, but currently doesn’t).
Honestly, I don’t know. It could be duplicate entries coming from either source.
AFAIR, you will also see “historic” duplicates which have since been merged with the main list item.
