With the exception of the githyanki patrol encounter, I generally do not mind the neutral NPC encounter designs. Giving up a guaranteed surprise attack round for an opportunity to talk with NPCs seems fair. However, I think it would be better if there were more opportunities to make a slight of hand check to try and get the jump on NPCs that you expect to turn hostile.
The gith patrol encounter is messed up because the dragon and dragon rider leaves the scene, even if you launch a surprise attack against them or Kithrak decides to kill you. I really hope that encounter is redone so the dragon stays and kills your party, if combat is initiated. The dragon should only leave if the gith patrol decides not to to attack you.
The biggest issue is accidentally turning NPCs hostile in places like the Druid grove, resulting in having to slaughter everyone in self-defense.