BG3 was never marketed as a strict DnD 5e game. It was marketed as an RPG "based" on DnD 5e. According to Larian it's meant to be a hybrid of RPG and 5e. So, if someone asks for an option, it shouldn't be a big deal.
Sorry, but this needs a separate answer: no, this is not true. They did promise a faithful translation, with some minor tweaks to certain rules (they gave example) for better implementation RAI (rules as intended) when RAW (rule as written) does not work. They NEVER talked about any hybrid system, or a homebrew system. Whenever rules come to question during numerous interviews, it was always "5e and nothing more".
DOS system remained - as I think (and I can be wrong on it) - for their DOS audience, who knows Larian for DOS games and came to play yet another game in their system. But it clashes with 5e rules on a fundamental level and if you advertise the use of one system and people bought the game specifically to play that very system, you have to stick to that. Otherwise, it's a false advertisement.
I read from a PCGamer article that states that BG3 is based on Larian's interpretation of DnD 5e rules. They claim that Swen stated that there are some things you can't translate from tabletop to a video game. Also this is a quote from the article "Vincke says the game will be heavily systems-driven and Larian will be creating its own D&D-inspired ruleset. "We'll stay true to our roots, so we'll give players lots of systems and lots of agency to use these systems and try to accomplish what you need to on your personal adventure and your party's adventure." In a way that is a homebrew system.
If you look above that piece, you will see that they were talking about imitation of DM's presence:
"
The Game Master mode and
co-op effectively let you play a tabletop RPG on your PC, but even when you're playing alone it can still feel like you're doing so under the gaze of a Dungeon Master, hoping they'll let you try this brilliant new idea you've come up with. The sheer variety of systems and Larian's willingness to let players bend or occasionally break the game leaves so much room for ingenuity. Vincke loves to talk about players solving conundrums in ways Larian had never even considered, and it's exactly like listening to a proud Dungeon Master gush about their party.
Baldur's Gate 3 will similarly give players lots of tools and then let them have at it. "We'll stay true to our roots," says Vincke, "so we'll give players lots of systems, and lots of agency to use these systems and try to accomplish what you need to on your adventure. That's not going to change; that's the core of what we're doing."
This is not about general rules that the game itself follows. On the contrary, if you check that article, for example
https://www.pcgamesn.com/baldurs-gate-3/dungeons-and-dragons-fifth-edition you will see at the very beginning "Baldur’s Gate 3 will be a faithful adaptation of the tabletop’s fifth edition rules".
So, no, the general rules were announced to be DnD 5e. They can not take it back now.