I agree absolutely.
Fit the MX5 box, then clean up all the bits needed to fit the Rover box, perhaps even get a re-conditioned Rover box if the original is beyond repair, and keep for the fastidious collector who might want to convert it back.
Is the MX 5 box strong enough? As has been said, torque is the issue. Well, the MX 5 box is the one bit of the M3W transmission that doesn't seem to fail...
Talking to my MX5 obsessed pal he says that the box will take 200 ft/lbs for ever and up to 300 ft/lbs if not thrashed.
How much torque does the Rover V8 used in the car produce? I'd guess no more than 250 ft/lbs. So it should be fine.