SvdM. Good observation, but no.
I have the template applied exactly as it is intended. The "Rules" of application are:
• Scale the template up or down, without changing its relative ratio, to match the height of the vehicle from the bottom of the tires to the highest point of the roof. Then align the templates bottom chord on the bottom of the tires.
• Align the template, front to back, over the vehicle so that the highest point on the template matches the highest point on the roof.
As I see it, what this does is allows for the shape to be applied to vehicles of differing height. Since a taller vehicle is going to raise the air up higher when it passes through it, the air is going to need more time to get back down on the rear of it after the vehicle has past. The template self adjusts, adding length to the extra height by scaling it up.
When I aligned the template in this GMC, I did exactly that. I went back to confirm it, and if you take a straight edge, and lower it down on the top of the roof, it hits within inches of where I place the top of the template. If anything, the straight edge showed I could move the template further back.
When deciding where to put the template, the existing shape is not a consideration. Very often, and as is the case here, the vehicle shape drops below the top line of the template. Does this mean we should build the aero cap to match the line at that point just behind the C-Pillar and stick up a bit? No. We just want the front of the cap to stay flat/flatter long enough to meet the curve again, and then ideally match its shape.
The cap would then look like this.
Here's a link to a bigger version.
Larger Picture of Denali with Top Line & Cap