Yes, 40 years of experience and knowledge are bottled up in the template. You can deviate significantly and get 8/10 results...few people have to knowledge to guide your design, and those that do won't do it for free. It's very high level and specialized knowledge - hence expensive. More kudos to Phil for releasing the template.
There are many ways to skin a rabbit (respect to my cat). The thing that drmiller said about moving the peak back is what Morelli did 10 years ago. At 0.25 there is "lots" of creative license. Aero is counter-intuitive and not easily grasped. OEM's super computers aren't adequate to cite an exact Cx - much less a casual glance at a picture. They still mete it out for hundreds of hours in the wind tunnel. Starting with an ideal body is easy. Starting with a real car is complex and no one can tell you what will work or not. I don't feel so dumb because top researchers can't either
It's either: study mech eng for a few years, make a bunch of prototypes and test over the years, or pay someone for their knowlege and skill if you want it now. Or accept whatever results you get.
George, like nasa said, aero is 3D. We don't know their full design intent OR their results. It's pointless to speculate. I also think you didn't line up the template properly with the lift body. My .02