Hi, Christopher,
I wouldn't worry at all, for one thing, our 7 string pickups have the same spacing for bridge and neck, so the pole spacing is fairly generous at the neck and should accommodate that angle just fine. Secondly, although it is ideal to line the pole pieces up perfectly, it won't have any disastrous effects if it's not exact, for example, LOTS of guitars with wide, 53mm bridge spacing have 50mm spaced pickups fitted (for example, my Ibanez RG550 had a 50mm bridge humbucker from the factory) and it works just fine!
You'd struggle to find a Fender Strat where the poles line up.. All 3 pickups the same spacing, with the one in the widest, bridge position angled!