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.
I have no clue what the licencing deals are, because they are commercially confidential. However, the fact remains that new content has appeared for old rules systems, and WotC have not created friction.
Similarly, since the 5e TT rules were introduced, I have seen 4 new videogames using DnD/FR branding that don't use ANY of the DnD rulesets, never mind 5e.
Even the videogame that WotC themselves released uses poker-dice mechanics rather than DnD rules. It seems to me that they are most focussed on ensuring that the current FR Story/World State/Characters that accompany their 5e games is used consistently, rather than making everything use the 5e ruleset.
WotC have said themselves that they want people to consume the DnD/FR brand in whatever way appeals to them, and have made it available in many forms other than just the TT rules.
Solasta seems most clearly a videogame product designed to appeal to TT players, whereas the "Larian-style" DnD seems less clearly liked by TT players.
But maybe TT players are not even the audience WotC want to reach with BG3? Maybe it's the several million that played BG1/2? Maybe it's the nearly 20 Million that have played ( or still play ) Neverwinter with it's modified 4e ruleset? Or the tens of Millions that choose games based on recommendations from the videogames media, who are less likely to be effusive with a strict 5e interpretation?
Or maybe "Dungeons and Dragons:Dice Adventures" is the shape of things to come? Perhaps it's foreshadowing the release of an all-new 6e Ultra-streamline edition DnD based on poker-dice ( just $49.99 fo a full set!).