The setting you describe for BG1 sounds bucolic but how can a group of nobodies become semi-gods over the small timeframe a game takes place? Which they do. That's actually nonsense, more nonsense than to be accompanied by a vampiric elf and been confronted with mind flayers at start.
What semi-god are you at the end of BG1 ?
Sure it is a "small timeframe" but after hours (and days/months in game time) you're still far from being able to fight mindflayer and bulette and drows and so on.
Things are brought a lot more slowly and the plot as a whole develop a lot more gradualy.
We don't have the full story yet but in my opinion the plot in BG3 act 1 come to a end a lot too fast. There's no more surprise /reveal after 3 to 4 gameplay hours.
(Especially if you're not playing with the tadpole and don't even have the dreams).
Obviously the mind flayers are not the main threat of the game, at least I hope so. They are overused as "the enemy" and boring, and that's of course also the "fault" of earlier good games which used them.
What other game could have a reason to have a logo designed entirely arround mindflayer ?
In BG2 we only see them for a few hours (1 map dungeon) because we are forced to go in the underdark but they are not really part of the main plot.