Warmoth don't move their pickup routes around. All the positions are programmed into and carried out by CNC, so there are no variations.
What you can do, however, is buy a pickguard that has no bridge slot cut out and then cut out the gap in the pickguard yourself, or if you ask some custom pickguard companies (just search Google for 'custom pickguards [insert name of your country here]' and you'll find loads) they might be able to cut the slot for you, if you can provide them with an accurate drawing of where the P-90 is and where the bridge cut needs to be. (They can't just guess it, they'll need measurements or a template from you.) To do that the best method would be to wait until you have the guitar body and a standard pickguard. Put the pickguard on the body with the P-90 in place and measure the gap between the pickup and pickguard. Then trace the pickguard onto a piece of paper but 'fill in' the bridge gap to fit the P-90. Most pickguard companies can then use that tracing to cut you a new guard with a bridge cutout that fits the P-90 exactly.