Ok, so I actually got this to work. Seems like you have to give the NPC 1 level in the Commoner class in his first class slot. So you put his classes in the 2nd and 3rd slots. This has the downside of only letting you setup NPCs with 2 classes but the prc classes do seem to work.

Also, when first using an ability from the NPC he will get the PRC Skin and Hide items and then you will have to force rest them so they can actually cast their spells.

Hope this helps some other people running into the same problem. While the AI can't use most Prc stuff, you should be able to use it against the players as the DM.

Fake Edit: I only tested this with the templar so I may be wrong about it working on other classes.