Yeah, it's pretty common to have the pickups higher on the treble side, so the volume of the skinnier strings matches the fatter strings. Another school of thought is to have the bridge pickup higher on the bass side, and the neck pickup higher on the treble side, to give you a grittier tone on the bass and a more "singing" tone on the treble, for solos.
If you want to preserve the setup, you can raise or lower the pickups without changing the angle--just count turns of the screwdiver, and make the same change on both sides.
It's your bass, feel free to turn the screws!
Ed