"Speaking as a gay man, I honestly don't think I'd have been as offended with the pick-up scene if (1) it wasn't notable flirt and porn addict Fox Mulder playing dumb and (2) in an episode on Fox with Doug Savant as one of the main guest stars, it ended with Dead Gay Matt finally getting a gay kiss televised."
I didn't care for this scene either because it felt sort of silly and forced, but FWIW, I thought Mulder's reaction and behavior here was totally consistent with his general obliviousness about social cues. What was that line Scully had in Detour? "You know sometimes, Mulder, I think you need to work on your..." How many times over the years has he missed obvious cues from Scully (whom he knows better than anyone in the world) and everyone else (for example, that woman who was hitting on him in Chimera). Mulder's not really a student of human behavior. I love the guy, but he's too self-involved and in his own head sometimes to pick up on clues that would be totally blatant to 95% of the population.