Dex hasn't stated that the mega drive version isn't allowed...
The problem is the Mega Drive version isn't an exact port of the arcade game; it's got a number of differences from the original, just like how Grind Stormer arcade differs from V-V arcade with bombs instead of powerup meter, faster bullets, etc. For instance, the
box in Stage 3 drops a 1up it seems in MD V-V whereas in the original arcade you have to
not destroy the large box in order for a 1up to appear later in Stage 5. There's also this
enemy in stage 1 - it's missing a whole set of bullets it normally fires at you in addition to the destroyable missiles, etc. That's all in addition to the screen size being changed, some other changes in enemy behavior/patterns, etc.
Considering the hardware the MD version's a good port, but it's too different from the arcade version to be acceptable in a scoring competition.