I can't imagine it being that big of a deal. I had a reputable PRS dealer tell me that routing had to be done just to swap out stock PRS humbuckers with another variety stock PRS humbucker (and they did said routing). The pickup rings cover the routing - no refinish is needed.
I kinda feel like I'd rather just buy a 408 than go through the trouble. I've done a refin. I've done a fair amount of minor mods to my guitars. At some point there will likely be a decent amount of used 408's on the market if the model goes as well as PRS would hope. I'd rather just wait it out if I didn't wanna spend the $ on a new one.
I'd be willing to bet as lame as all the dealers in the Phoenix area are, there isn't a 408 anywhere for me to even go try out. <sarcasm> I know we're not a bustling metropolis like Lacrosse, Wyoming or something. </sarcasm> They have one down in Tucson at Rainbow Guitars, a Sig Limited, if I only had an entire day to devote to driving 250 miles to try out some new pickups.
So, would I have a guitar modified to fit aftermarket 408s? Maybe, maybe not. It depends on how they sound, and I would need to go try them 1st.