Good call Nabterayl, cover saves are on a model/target basis, not by model "type" under the section about the shooting phase. So any model or target, regardless of it's type, gets a cover save if it is obscured 25%, in area terrain or has intervening models in the way.
Now, what about the wording on Melta? It seems safe to say that Melta doesn't work against Fortifications. Even if one argued that shooting at them was handled "just as if" it were a vehicle, that only covers shooting, not penetrating/wounding.