He called her Secretary Clinton for a couple of reasons, I think - to offset the sexist reputation he has (from the things he has actually said), and as a reinforcement that she was Secretary of State when she made the mistakes he wants to focus on. And "secretary" has a different meaning in his world...there's that little nuance. He was trying not to be insulting by pointing out that he decided not to mention things that would hurt Hillary and her family (although I am sure she was quite prepared if he did) and I think that's really the best restraint he's capable of when his ego gets hurt. But he has to announce how good his temperament is, anyway - because it's hard to see with his actual behaviour, but we should believe him anyway. He's very childish.
And I don't think they are in the same league. If it's for show, Donald made it a show, unfortunately.
Let's not forget that he asked her at the start of the debate if his calling her Secretary Clinton was okay and that she agreed that it was.