I have a rear-routed Deluxe 5 with 2 Musicman pickups ... no extra charge to route.
However, my top-routed Deluxe 5 does have the standard J pickup in the neck. I know that Warmoth only does this route on their Deluxe 5 pickguards.
If you feel brave enough to cut your own pickguard, you can certainly ask for a different neck pickup route, although it does not show up as an option in the body builder.