A friend and I have just started playing GSB. He mentioned something to me and it seems very odd. The Tutorial Cruiser has modules on it that you cannot add yourself (presumably because they are locked.) However, you can change the other modules and save as a different ship. The example he pointed out to me was automated point defense and powered armor.
It would seem that you should either be able to use this, or not, but not be able to trick your way around it by using the Tutorial ship as a starting point.