The baritone neck has 23 frets to the heel, so the bridge isn't as rear shifted as you might think, I think it was around 12-15mm when I worked it out.
But you're also right that I'm planning on largely ignoring the existing routes in the final build. I'm going to put it all together with the kit loaded pick guard first and see how I like it, then I'll probably reshape the body and swap to a mini-bucker and probably two P100's. I'll use as much of the existing route as I can, but... as you say if it needs to be further south I'll just make a bigger hole.