So just to be clear I did NOT say your louvers where distorted, I said that it looked like your louver rim seal/gasket was possibly deformed, and made this assumption on the pictures you posted which are thumbnail posts that can not be opened up in MS Paint, and from what is visible in your pictures to markup for you, your louver rim seal gasket does not lay flat like the one in Brians picture or in my louver seal picture. I also gave you very specific details using Brian's picture to show how the louver seal sits down flat against the glass and fits against the SS window trim, which to me is needed to correctly locate the louvers on the rear window to locate the rivnets.
My car did not have louvers or a rear spoiler from the factory, so I sourced OEM parts and installed them 30 years ago and positioned the louvers with the hinges mounted on the louvers by placing the louvers on the rear glass and using the SS trim and the flat louver gasket as my positioning guide and then marked the rivnut locations through the hinge holes with a drill of the hole size. Then removed the louvers drilled pilot holes and then rivnut size holes, brushed some primer/body paint on the bare metal holes, installed the rivnuts and screwed down the hinges with gaskets, and the louvers fit perfectly.
I am not sure why you are so caught up in putting the rivnut holes into the roof before you have installed the window trim, I would finish the body and paint work and install the trim and then install you louvers. You are trying to position and install your louvers prior to installing the SS trim which is the perfect locator reference. To compound your efforts you are using an aftermarket glass gasket which has been proven time and time again does not fit properly and you also using an aftermarket louver seal which you yourself have seriously complained about. So with all these issue creating variables, and the information provided, I am having trouble understand why you are still not understanding what could be causing you louvers not to be sitting correctly.
I have again posted Brian's picture with my comments circled, and I have also posted pictures of my louvers and the rim seal shape laying out flat and giving the 1/2" to 5/8" spacing referred to in the thread and you are very surprised at?? Also a couple of pics of my present rivnut install. This will be my last post on this topic and hope the information provided by myself and others will help you resolve your problems.