Update, but OMFG...
The glass was installed last week, after a month. Took 3 hours (they had issues, glass worked itself into the rails), but it is in, waterproof, everything seems to work fine.
Bad news is the headliner was full of glass, and the glass shop does not have the skills to do that, so got referred to a body shop they use. Took the car to the body shop at 8AM, got a loaner car, got a call at about 2PM and they said...there is a VW-specific tool needed to pull the grab handles and sun visors, they don't have it, they have ordered it, and I can come back once they get it. That was 100 miles and 2 hours wasted making two round trips for that. I do appreciate them being open and honest and apologizing.
So, maybe next week, week after I can get it finally done?
Insane, what a PITA..