My prepared car has no trunk floor, which was removed to allow for fuel cell installation (17.2.E). SM rules allow modification to internal body panels to accommodate a fuel cell (16.1.D.3.D.2) but the modification can serve no other purpose. This is made clearer in 16.1.P where changes just for weight reduction are prohibited. So I would say that you cannot simply remove the spare tire well in SM.
Hope that helps,