I'd forget trying to mask the interior of the canopy - too hard for the reason you spoke of.............
Just mask the outside with BMF, spray the interior color first (zinc chromate or interior green I presume), THEN shoot the exterior color - Olive Drab or silver or whatever.
When you look through the canopy (like from the port side to the starboard), you'll see the interior color on the inside of the canopy. Unless it's a huge scale model, it's unlikely that you'll be able to tell that the interior color is actually painted on the outside.................
Cheers,
LeeTree