If need be, I suppose you could always maintain the covert aspect by reasoning that mobile bases really just represent a bunch of support staff rocking up to a location (disused warehouse, whatever) in a series of tricked-out vans and trailers, and just claiming it as a temporary base of operations after fitting a few spotlights and scribbling a bunch of plans on the nearest whiteboard. Just like in the movies.
Maybe differentiate it ingame by having it only use very limited facilities, and maybe having no innate defense against alien attack. Or maybe just having a base defense equate to a terror mission, after which the location is lost (or compromised if you prefer) and surviving personnel are shipped back to the nearest 'proper' base.