I can see the construction of a new hole in Nevada attracting Soviet interest so, of course, it must be a new military installation and thus deserving a couple of MIRVs.
Perhaps it would be more logical to go with a mine that is worked for several years and then closed.
As far as if this is THE Prime Base, or the Alternative Prime Base, perhaps it is the facility were Bruce parked all of the old Council of Tomorrow as they reached the end of their usefulness, just gives the PD more ways to entertain the players...