I think I would be inclined to get the pickguard routed for the pickup only and drill volume and tone myself to be on the safe side. It also needs to be taken into account where the side jack hole will meet the volume and tone cavity so that placing a tone pot where a pickguard mounted output jack would go does not clash.
FWIW, I have a PJ P-bass with four controls, and a side jack. It all fits. Ironically, I never touch any of the controls at all and wish I had the jack in the pickguard and a simple on/off toggle...
Additionally, I've swapped over jacks and pots on many other guitars, including Jazzmasters, Strats, LP Jrs and SGs. As long as you use short-shaft pots (as is standard for pickguards), a pot won't take up any more space than a jack will. In fact it's only the other way around which has caused me problems; sometimes a jack doesn't have enough space where a pot can fit.
Though as stratamania says, these are the sorts of questions which are most conclusively answered by Warmoth's customer support.