I wouldn't worry about it too much. The Template presumes taper in plan to equal the taper in elevation, and a half-circular cross section. The racer's aphorism is "It isn't how you punch the hole in the air, it's how you close the hole in the air." IOW the rear is more important than the front.
That said the bluff forebody of the Template insures the flow is uniform enough that it can support the taper without shedding vortexes. Any disruption such as the windshield header you mention can spoil airflow 'downstream'.
Why not go with the curved header and then a Tropfenwagen style rear with a flat top and tapered sides? It would have more interior space.
