Currently, only Doom 2 BFG edition automatically recognizes "nerve.wad" as a separate episode. To use it with the original commercial edition, you have to manually add it in .ini and it works without problems. Took me a while to figure out why it didn't recognize this episode only to realize I needed BFG edition.
The default IWAD definitions only autoload companion WADs that were required by the official releases (ie. voices.wad for all Strife versions). Anything beyond that is frankly a matter of the user's taste, and best left up to them.
Huh, I didn't even know there was first-class support for nerve.wad. O_O
I'm kinda torn about this -- on one hand, it's a cool feature and it's kind of a shame that it requires using the bootleg-quality BFG Edition IWAD in order for it to work, but on the other hand, it's technically accurate to the release versions of both games. Damned if you do/don't/etc, I guess.
You can just autoload nerve.wad with Doom 2 and it recognizes the addon automatically and renames the mapnames so they work with GZDoom's internal episode definition anyway.
In the interest of not being a boorish asshole and forcing this change, I simply PR'd it for approval. I've tested it - and it works (did I really expect it not to?), but with and without nerve.wad present. If it's there it simply loads it, no biggie.