Is there any way to separate these two values? For instance, as an anti-turtler move, I would like missile infantry to take only one spot in a transport, but two in a structure.
Actually, I believe that the GarrisonContain module ignores TransportSlotCount. Even if this is the case, though, then unfortunately you still can't do what you suggested as the missile infantry would still take only 1 slot in a structure.
But if you want to weaken the Bunker, then I suppose you could start with doubling (or tripling?) the build time.
You could make the missile defender take 2 slots ( assuming that will actually work in buildings - CommieDog suggests otherwise ), and then increase the volume of the transports to accommodate by a multiplier of around 1.5 - to prevent too mant cheap units fitting in while still accommodating the larger units. But the exact number could be taken from playtesting.
Other than that, like I say I can't see another way of doing it.