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.
I think players often project their own assumptions on WotC that are not necessarily true ( unless you have some solid evidence to suggest they only want 5e products, of course ). WotC make money from all DnD properties, and they get publicity from all DnD properties; why would they not want that ?
SoD was developed as DLC for the old game. The NwN module is DLC. That's not the same as a new game.
Beamdog has literally said themselves that using 2nd ed for new products is off the table. WotC doesn't want it, they want to promote their current line of dnd.