Well, as pointed out, just because a show called "X-Files" exsists in their universe doesn't necessairly mean it is "OUR" X-Files.
I think that's stretching it just a bit too far. You know, Occam's Razor and all that.
Although if you want to run with that: Just because a detective named John Munch appeared on X-Files doesn't mean it's the same John Munch from L&O/Homicide...
Ah, but we're shown in the X-Files episode a very similar style and setting as the series meaning we're supposed to infer both are "in the same universe. But having a show called "X-Files" in Homicide's universe doesn't preclude the exsistance of Mulder and Scully and their adventures as we're never given any details of the show other than one of that name exsists.
But, for the "fun" of this exercise I think we can ignore these little slips in contnuity. (Along with George watching "MAY" in Seinfeld and other slips in the shows.)