I like the cover. It's a lot better than the bland cover for ROTF that's below it.
But besides "Little Green Men", Star Trek has another connection to AREA 51. Jonathan Frakes made a documentary on Roswell back in the late-90's. As far as I know, it has only been released on DVD by Front Row Entertainment with poor audio quality (the audio is very muffled).
As for continuity, I was thinking more of the Greg Cox continuity from the "Assignment:Eternity" and the Eugenics Wars books.