If your working with an architect, just give him the finished dimensions you need. Just make sure that he understands that you need the finished space to have that clearance, not the construction measurements.
You may tell him that you want the garage door to be 12' wide x 14' high, but after installation and trim is added (maybe ramp up to), the actual opening may only be 11'6" x 13'6'.
Better a little bigger, a few extra dollars , than built just to size and when finished, the MH doesn't fit by 3" or so, then big dollars to modify.
Ken