We see Mary mention her thoughts about his original letter out loud.

It is possible that during his pompous nothings, and apologetic boasts, she made her approval known. A simple nod of understanding, or a spoken, "I have often thought that, as well," would be clear enough, without her having to be obviously set on him (the way she was in P&P2, for instance, when she preens whenever he is nearby, seeks his conversation, and hopes he will ask her for the first two dances at the Netherfield Ball!).