Mulder raises an eyebrow, making no effort to hide his dubiousness - but all the same, nowhere near saying no, no, I'll go lay on a hardwood floor somewhere else.

Scully sounds like she's made up her mind. And yet, he can't help asking, "Are you sure?"

She's stubborn, but the synchrony marks a pretty significant difference between motel rooms in the boonies and falling asleep side by side on the planet of casual sex. There's a sensual component in general, if not for them personally - and if they kick dirt over the line, Mulder's not sure they can unkick it.