So I bought the interior assembly manual to hopefully clear this question up. In the artists rendition it actually looks like there is a trim plate put around the carpet, prior to the console. On the page showing the console install it has the shifter listed, and refers to Body engineering installation manual.
I did cut my hole precise to fit the shift boot, and it looks ok when in neutral, but when I shift (3rd and 4th looks worst) the boot pulls enough that you can see the cut hole, and I mean I got that cut out about perfect to that boot.
Also wondering if anyone has any photos, or is Mustang is similar, on how the carpet gets cut/trimmed at the bottom of the quarter trim panels? Is the panel to go over the carpet, or just enough carpet left to fit in the little indent along the bottom edge of the panel? The page showing the installation of the panels does not show the carpet in the car.