The Milspec armor's Armor is Hardened Armor. It doesn't have different values, just all of its armor is considered Hardened.
As for Drakes, nothing that I'm aware of would restrict the ability for the worn armor to be effective with the natural armor, so by default they would stack. That being said, as a GM I would probably put my foot down restricting the ability for Milspec armor to be modified to allow for Dracomorphosis. Personally, I think the "added flaps and gussets" (or whatever it says) would be contraindicated by the Custom Fit.