The trouble is when I think about it I can't help but see flying a Spheroid(Small Craft or Dropship) would be very different inside an atmosphere than outside it.
Aerodynes(again Small Craft or Dropship) I would see using Piloting/Aircraft in atmosphere.
ASFs, Aerodynes, and Spheroids would use Piloting/Spacecraft in space since Battletech does use a physics based model, or at least tries to I should say.
To compensate I'd take a two prong approach of probably making it easier under non-combat conditions,possibly in general, and probably would advise that a player invest more in the atmospheric skill than the space skill since space is big and consequently less important to have really good skills for.