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.