I think what RunAmok meant is can you use the exterior and put an interior in it. The rabbit hole buildings can be edited on the outside (more trees, benches, etc) but I don't think you can turn the rabbit hole building into a playable building.
But if you wanted to redesign your rabbit hole building to still be criminal hideout but look different you can use the moveobjects cheat, place the warehouse in a basement and build a new criminal hideout on the surface. Though you would still need access (stairs/elevator) to get to the warehouse which is hiding underground. (or to save on space, the new town Lunar Landing has new rabbit hole entrances which take up a whole lot less space as they are just doorways).
But I don't think you can edit the premade rabbit holes.
But awesome idea though.