He is not Mulder. He is her F.B.I. partner, but we never find out his true name. He is very focused on her, very concerned for Scully, because he knows what we are soon to find out, that one of the people who was taken, who has yet to be found is her former partner, Fox Mulder.

Scully is clearly pretty shaken up by all of these returnees, some alive, some dead. She must be terrified in fact. Will he be a stranger, like the ones who are returned alive, barely functional, nearly catatonic. Or will he be one of the "strange dead"? She calls her partner "Mulder" by accident, which is very upsetting to him. "I'm fine, Mulder." How many times have we heard her say that? Well, clearly she's not fine this time, but she isn't going to listen to her new partner any better than she did her old one. She has confirmed for him that she is indeed too close to this case, so close that everywhere she looks all she can see is what she has lost.

The parallel to Jess Mabe's "The Other Man" is striking, and not one I had considered.

You did not miss anything. Kipler wants the reader to think they are reading one story and then come to find out it is another story altogether. The other story that comes to mind in this genre is "Cellphone" by Marasmus. This one is even more of a shocker though, at least it was to me.