The only reason for them right now is for the achievement. But I'm gonna start using them in coming updates.Half correct. If the Player was to choose nothing but agro in S2 it wouldn't matter at all to the dialogue "flavor" though. So, every Trait choice in S2 makes no difference at all in it's current state. If you wish to alter that then (as previously mentioned) you could always add them together if you desire ("friendly+friendlyS2" for example).
Keeping achievements separate makes sense though, so I'm on board with that perspective. Chew on it. It's nothing game breaking but there's really no point at all in the 15 Trait choices the Player makes in S2 currently (besides Achievement unlocks)... just know it's a thing.
I do agree that checking friendly + friendlyS2 would've been better than just checking friendly but there aren't gonna be any big problems because of it, for example if the game sees that you've picked mostly friendly options in S1 and alters the dialogue because of that, even though you may have more of witty if you combine S1 and S2, you'll still have chosen a lot of friendly options and MCs dialogue will still make sense. As I said these are only for flavour