I'm assuming that when in the middle position, the neck volume pot becomes a master volume for both pickups.
Actually both (or either) volume controls will act as a master volume when in the middle position on the switch, and both tone controls will act as a master tone. So if only the neck volume is working that way, there is still a problem (that have no advice for).

As mentioned in the link you posted, there are wiring schemes for independent volume controls, but the way it's wired now is probably the most common. My PRS1-TS build is wired per the PBG diagram and I don't find it a problem. It just is what it is. Then again, did I mention that I'm a strat guy???