I don’t think “have a seat” really means have a seat. When my boss told me to his room, he always ask me to have a seat, then he start complaining lot of things. I visit my friend, she told me “have a seat” then she start gossip about her friends. My boy friend’s parent ask me to have a sit, then start asking my family background. So now when people ask me to have a seat, I will said “ I like to stand”.