Personally, I'd rather have lookup by series and episode name (which TVDB definitely supports in all cases I've seen), but the current JRiver "get" function doesn't seem to accept (at least I haven't been able to figure out a way).
The problem with that is that matching names is rather fragile, you need the proper spelling or it won't work at all, and many people don't have episode names in their file names - or the file name doesn't support all special characters and they get changed, and the lookup breaks. Or you have to go and fix that manually by looking at TheTVDB, which defeats the purpose really.
Using the episode number is just much much simpler for lookup.
I've only a few shows in my library where the air order and dvd order are different, and I had to re-order them for lookup manually to fix it, but it was somewhat of a rare case that they changed the order that I didn't really bother to think too much about it, as it would mean quite a bit of complexity as well.
I suppose I could try to re-visit this topic, and simply add a checkbox in the two lookup dialogs to enable DVD order.
This would then only work for manual lookups, since it just doesn't know any better during automatic import, and not changing the default, since who is to say DVD rips are more common than TV recordings, but should be much easier still than re-ordering things.
It doesn't help though that TheTVDB uses different formatting for the DVD Episode number, ie. in Firefly its "1.0" instead of plain "1" - another point against using it as a default, since that field is barely maintained on many shows.