I also think this part of the fic is about...hmm...I suppose it's that Scully's psyche is utterly suffused with the horrors she's seen. As she says, she simply has no room left within her for any more pain or horror. There is no safe place for her, not even in her own mind or body - no 'sacred circle' she can fortify herself with or talisman of sane fact she can hold fast to (I'm considering this in relation with the future Scully of Weret Hekau). There is nothing untouched by trauma. Thus, she can't draw a seperation in her mind (or body) between herself and the alien that had begun to grow inside of her. She has been invaded in violent and unimaginable ways, and she's instinctually thinking about that. She's barren, and Mulder is coming inside of her, and she's wondering if an alien, which destroys the life it grows inside of, has a concept of what a mother is.

This is the best reading of this line that I can imagine. It blows me away, really, it does, but it makes the story even grimmer.