The githyanki encounter is messed up for more reasons than that, in particular that it's a major, inexplicable difficulty spike from out of nowhere. It's so far the only encounter in the game I haven't managed to beat.
I have considered the possibility it was intended for players who play as Lae'zel. I may accidentally have hit the intended behaviour for anyone else by my reasoning: Lae'zel has made it pretty clear her people consider themselves the master race, so they'll likely just kill you to get rid of the mindworm infestation. So in my first playthrough, I decided I could trust them only slightly more than Raphael, and never went there during the main quest. I visited the place later...to find people as dismissive as I expected, but also not starting a fight. Odd, that.
The Nere encounter is more pertinent IMO. At least if you don't reason that it's better to kill the duergar in order to free the deep gnomes before another potential enemy shows up, but instead think you need Nere so better not piss him off...and then all hell breaks loose with your talking squishy in the middle of a cluster of enemies. Because you didn't pass a persuasion check.