Beamdog are only allowed that leeway because they're working on a rerelease of an old game. It's not something they would be allowed to do if they were making a new one.
SoD was a new game, not a remaster. They have also created a new premium module for NWN. I am no more privvy to their commercial agreements than you are, but if WotC hated the idea, I would expect more public friction.
SoD was an expansion, not a stand alone game. It simply used the same AD&D rules as the game that came before and after in the same saga. For NWN, my guess is that it is a new module of an existing engine\ruleset. I also don't think they would be allowed to use 5E if they made a brand new game from the ground up.