Maybe I'm too much into meta-gaming myself, but there are some encounters that really frustrate me in this department. The chief of which is the dudes in front of the chapel. I can persuade or intimidate them off for companion approval, or I can fight them for xp and loot. I want to milk every drop of xp I can before the Grove gate fight, and not having xp awarded for skill use or role playing my alignment is annoying
But it's a really minor frustration, and doesn't affect my enjoyment of the game any more than the toilet chain does, it's just something I've learned to line with...
Which as I write that, I realize it's exactly OP's point. Yes, Larian are encouraging killing over problem solving on other ways, but only for those who are valuing in-game rewards over their personal satisfaction in role playing