Frasier thinks that just because Niles "broke up with" Martin right in front of Emily, that everything will be ok with Emily in the future. What about when she comes back for future dates with Frasier and sees Niles there, sees him for who he really is (Martin's son, not Martin's ex boyfriend)? She'll find out eventually that Frasier lied to her about his dad (who pretended to be gay to get Emily's mom to back off).
In every other episode, Niles always knocks first when he calls at Frasier's, but he comes straight through the door at just the moment Martin needs him to.
Martin takes a jab at Frasier by agreeing that his situation is a "Sophie's Choice". This belies his blue-collar-Joe-six-pack persona. He would not be familiar with the novel or film.