There have been several instances of this breaking the rear window in the S and 3, I not sure I would consider this based on that evidence alone.
Also if you are torquing it at an angle it wouldn't it compromise the seal, but I'm not entirely sure I know what anchor you are talking about... sorry I may have misread the original post or don't entirely understand what you are asking?
I could see where putting an object in the seam where one was not originally intended to go causing stress on the glass and cracking it. Not good, especially if you are attaching a sucker to that glass. Attaching the seasucker to my glass roof already kicks up my worry meter a notch, but its well within the acceptable limit of worry. Putting this anchor thing in the seam and shutting the hatch would elevate this to level higher than I am comfortable with, until I see alot of people reporting on its use on Tesla Model S's, which I don't.
I'd give them a call and ask how thick the anchor plate is to see if it will fit the gap in the trunk/body seam. I've considered it, but haven't committed yet for 2 reasons:
1. My car is wrapped (advertising for my business) so I have some concern about the wrap getting beat up.
2. Assuming we put the plate on the side so it's away from the glass, I think any of us would need a very long cable to go through the fork end of the SeaSucker. If you just wanted to secure the bikes and wheels, a 6' cable might work.