I'm pretty deep into Act 2, but I don't think I've noticed any in-game effects from the various regional reputations yet.

 

Am I failing to notice a vendor discount in Defiance Bay, or something similar? Or are the reputations mostly just window-dressing?

I would like to know this as well. I do know that people will recognize you if your reputation is high/low, so there's that, but whether it gives you any actual mechanical advantage, I do not know.

If you have Eder with you, there's something you need to do in Defiance Bay that you can only do once your reputation there is high enough.