Mount hinges so that flaps are paralell when door is closed.
Screw heads are intended to be slightly proud, as this makes the strongest fixing and takes care of screw head diameter tolerance. Gaps between the flaps and centre part of the hinge are there to prevent stripping of paint when door opens.

Mount hinges on the door first then put a packer of about 1.5mm thick (a steel rule) under the door before marking hinge position on the door frame. This will give suitable vertical clearance.