There isn't really a preference, since it should work the same with either arrangement. You should be able to get the pickup to tilt with the lower screws in either diagonal position, it just depends on their relative heights. Make the screw under the bridge side of the pickup lower, it will tilt toward the bridge. These height adjustments depend on the screws all having the same heads.
The system is designed to be rigid and also for ease if replacing a pickup. When you remove the upper screws and the pickup, the new pickup will drop in at exactly the same height as the original.