It's only an issue inasmuch as it is an aesthetic issue for you. If you think it looks fine, great! If you think it looks wonky, then you need to either order one with pickups placed where you don't think they look wonky, or get used to the wonky-to-you look. I think it looks fine, but I don't see with your eyes.
Sound-wise, it's not an issue at all. If you were blindfolded and had to listen to two or three different P basses with different pickups, and a Jake, they might all sound a little different, but you'd be unable to tell which one was the Jake just based on the pickup placement.