Sven, I know this is nit pickish, but yeah, it's below template and I think rather significant.
When you overlaid your template, it was too low and a bit too far forward. According to Phil, we want to put the top of the template at the highest point on the roof, this is to prevent the arbitrary placement of the template. I have the underside of the my line right at this point, and it is above the rear door. Your line is into the body work at this point.
I checked the wheels for level, and they are (this can throw you off). I'm looking at where the bottom of my line is to judge the deviation, it does not do any good to cover up what you want to analyze in my mind. Also, I can assure you, that my template is dead nuts on to Phils illustration of the template from the peak back. It does not match the front precisely but I think we can agree that A) It isn’t nearly as important as the back, and B) It isn't really in question.
I have gotten very good at applying this template since I have done it many many times over the past year. (I see I made a mistake on this again in that I didn't hit the bottom of the wheels with it, but that, were it corrected, would make the gap a wee bigger on the back)
Below is a link to a high resolution image of the low res one here so you can more clearly see what you and I have done.
Svens Fit with Charlies Template Detail
I feel the 2½" to 3" deviation at the back of the roof line is significant. And when a Fit is seen in the wild, and you know what you're looking for, it is pronounced. My thought is still that this is an intentionally engineered feature that somehow works to help reduce the Cd, otherwise, I see no reason for Honda to have done it, they could have followed the template and would probably have been cheaper and easier to do.