For TV Show Extras/Specials, is there a way to just have them in a folder without giving them an episode number?

Not with Plex’ default scanners/agents.
There’s a user-built scanner that has extended Plex’ default behavior and allows addition of local media assets to shows, seasons and episodes (however those are not displayed in all clients).

You’ll still need to follow some naming conventions for your folder structures… and of course no guarantees.