The NPC generator allows you to scale the coompetencies according to the relative power of the PCs. You pick the threat level, so you literally could, using the same stat block, have a dragon turtle that would be an appropriate challenge for 1st level PCs, 20th level PCs, or anything in between.

All of the monsters were generated with this system and most of them are OGL monsters (so you could compare owlbear stat blocks).

Finally, there’s a fairly extensive OGL conversion guide in the rulebook.

How hard would it be to make NPCs using Fantasy Craft (keeping in mind I have no SpyCraft experience to ease the transition.) Would the resulting NPCs be comparable in any way to 3.5e heroes? It sounds like they’d have a totally different engine underneath– would it be easy or only moderately hard to correlate a built NPC to a 3.5 party for challenge purposes?

At one point I picked up Midnight on super-sale in hope of finding lootable monsters, but the different assumptions and lack of bestiary in the core book limited my ability to use it for a standard 3.5 campaign. Would fantasy craft have similar difficulty corresponding to standard 3.5?