Go wherever you have to go and play one first; on paper it sounds like a good idea, but I was real underwhelmed when they finally came out and I tried one out. Maybe it's just me, but I didn't care much for the modeled sounds from the Roland GK pickup. Don't get me wrong, they're OK, but the problem for me is that they're "just OK", not great.
You can see some of where the extra routing is done on page 15 of the owners manual:
http://www.roland.com/products/en/VG-99/features.html
It seems like the guts of the VG contain a subset of the features in the new Roland VG-99 modeling system
http://www.roland.com/products/en/VG-99/features.html
You could call/email Warmoth about the viability of having them do the routing, but they're so busy I don't know that they'd want to do a VG model routed body.
There would be a couple of other alternatives; for a few hundred dollars more than the VG you could build your "dream Strat", install the Roland GK pickup and get the VG-99 system and have all the VG sounds/features + a lot more.
OR you could just be like a lot of us maniacs on this board and build multiple Warmoth guitars with a variety of PUs/woods/electronics to get all the sounds you want.