But at the beginning, in the teaser, she's putting her clothes back on... She's at Mulder's house, and she's putting her clothes on. So yeah, she started out sleeping on the couch, but at some point she got up and took off her clothes. So...why was that, if it wasn't for sex?

I believe that he argues that she just took a shower. Which - you know, seems a little silly to me (I don't usually take a shower at a friend's place if I fall asleep after a late night staying over; I go home and shower there) but, eh, whatever makes him happy!