At work this morning, I took a look at my hatch and how it sits while putting my roof panel back on. With the hatch closed, the glass is about a 1/2" from the halo bar (i.e. roof) sitting on the gasket. In the back I'd guess the hatch has only about an 1/8" clearance to the car. When I raise the hatch, it looks like I clear the roof gasket by about 1/4". If I were to raise the glass (i.e. slide it forward toward the front of the car, that would increase the chances of it not clearing. If I raised the height (i.e. move the glass toward the sky when the hatch is closed), I'd be concerned that it would not seal tightly on the car. Do you have a big indent in your gasket, because that's what I'd expect if the glass were too low. If it is really low, I'd talk to another glass shop. There must be a gasket that the glass sits on in the frame. Maybe it compressed. The dealer's body shop will have the parts drawing which would give you a chance to see how it fits and what could be done.
The other thing I noticed is that the hinges rub against the gasket when I raise and lower the hatch. Make sure you tear is not occurring from the hinges having a burr or other imperfection.
BTW, I took a look at a video you posted a while ago. The video quality was poor IIRC. You consider redoing it if you are still seeking help.
