Say something like this:
ESB DE 2.0 BD25: Just the Film
ESB DE 2.0 BD25: Just the Special Features
ESB DE 2.0 BD50: Film + Special Features + Bonus Commentaries
ESB DE 2.0 BD25: Documentaries
The third one doesn’t have the Bonus Documentaries.
Perhaps releasing them as
ESB Disc 1
ESB Disc 2
ESB Discs 1 and 2 (Combined as a BD50)
ESB Disc 3