I have a 2008 EB with an SMB manual PH. Here's a couple photos and measurements for you.
The first one is at the rear barn doors, looking straight up. Due to parallax, the tape measure looks incorrect. The actual measurement from the bend in the J-hook eyelet to the rear edge of the exterior rain gutter is 11".
Here, I measured from where the padded panel opens into the penthouse area to the center of the windshield at the headliner. This dimension is 35".
In both locations, I believe the roof is cut open at those points, give or take a 1/4" behind the padded panels.
In the rear, the rubber gasket on the outside edge on the fiberglass shell lands on the roof just inside the rain gutter, so it probably overhangs the opening by about 9.5"
In the front, the top overhangs more. Measuring from the front of the PH to the same place on the windshield, there is about 18" of van roof exposed, which means that the fiberglass shell extends about 17" forward from the cutout opening.
Trying to estimate distances from the eBay post, I'm guessing that you may be okay with the rear sunroof hole and it will disappear when the roof is cut out. In the front, it looks like the PH gasket would be resting about in the middle of the sunroof glass.
EDIT: I'm an idiot. I misread and thought you wanted a pop top. Nevermind.