The Mission question I'm not sure on, but I imagine it'd be pretty much the same structure, though FantasyCraft will use a Cash and Carry gear system making "missions" slightly less important except for "N times per mission" class abilities and feats.
The structure will remain, though as Agent 333 says mainly for character ability balance. You could pretty easily fade everything else into the background so you're left with a lean, unbroken narrative. We'll probably include some guidelines for this, though it's a little early to say for sure.
Answered elsewhere on this forum, the default is to use the scaleable NPC system; so as the PCs get tougher, so does the dragon. Of course, if you want to set it at a specific threat level feel free.
There will be campaign qualities allowing static, non-scaling monsters.