Then there's the Dark Urge
camp scene killing Alfira. Come on, some girl is being eviscerated, she should be howling in pain and fear, and none of your crew really does anything? Same thing happens at the Temple of Bhaal, your team sees you accept Bhaal as its new Chosen. You virtually choose to replace Orin as a chosen and swear to dominate and murder the world, and your teammates just STAY??!!! If you choose to kill some tiefling refugees, Karlach, Wyll, and Halsin are gone and both Gale and Shadowheart are displeased, but somehow swearing to murder the world and become an Orin substitute doesn't cost you none of your allies? WTF, this is really bad writing. This choice should pretty much cost you everyone but Astarion and maybe a Shar aligned Shadowheart.
My other problem with that design is not about narrative coherence, but about what it does to your gameplay. You just enter a state where you rush to Orin and ignore all intervening side content because otherwise it costs you dialogue with whoever she picks until you do what needs to be done. It really railroads your play.