MC40 starting with two troops has to do with the ship slot it's in. Since it replaced the Medium Transport (I think) it starts with two troops even though it can't hold any. Similarly since the SSD was placed in the Galleon slot, it's possible to start the game off with one (I've had a game with 3 starting) even though it hasn't been researched yet. And just like the galleon in a 'regular' Rebellion game, it starts off with two troops. Some weird coding somewhere in the game I think. Either way, just a small annoyance, cause once you move the troops off the MC40 you can't put any back on.