I think, if you go back far enough, the bartender's comfort and safety does play into the hight (along with the safety of the bottles)
Having a bar with that hight creates a real barrier between intoxicated sheninagens of ones coustamers. Fights and idiots are more likely to stay on the other side, if your barrier is high enough. Also, having actual seating is a relativly new thing. The hight of the bar is equal to having a surface comfortable to someone standing, which is a good thing for coustamers who don't have a chair.
So when seating became more commen it was built to fit the bar already in place rather then redo the bar for the seating.
This is purely conjecture, but it makes sense to me.
And, fyi, I like those seats. I can be tall for a change.