Oh OK, I see what you're saying. I think my plan for the roof rack is the same as what you're saying. The rack will run the full length of the roof. The front will match the windshield and from there will match the template. I will then have a removable kamm that can attach to the rear end of the rack to extend the template even further behind the truck.
EDIT: I think based on this template with an imaginary roof rack, it might be better to angle the front of the rack backwards just a little bit more than the windshield. I think that might help keep airflow attached around the "corner" of the windshield/roof angle. Although, at the same time, the windshield seems to be pretty close to the template anyway.