My strings line up exactly the same and I have noticed this on many guitars over the years and I don't think it really matters. I am VERY annoyed at the difficulty there is with re-stringing the stop-tail especially the non-wounds. It is impossible to do this with the pick up in the way. I have resorted to releasing tension on all the strings then detaching the stop-tail all together so I can see to guide the string through. This really is stupid. And I have searched the net to see if others are having the same problem and this is the only reference found so far. This seems pretty odd, or have I missed something? This is my only criticism of the SE Akesson but this one thing is really pissing me off! Help...
Step 1: Remove offending pickups
Step 2: Bend the pickup legs just a bit
Step 3: Reinstall and marvel that the strings cover the pole pieces, and sounds exactly the same!
You're welcome.