So, just to close the loop on my cracked Model S cracked roof experience, after initially taking my Model S to the SC on 24-May, I finally got a text on 2-Jul from Tesla that the replacement roof had arrived at the SC and to schedule an appointment. I wasn't able to take the car in until the 19th.
The replacement was done in a day, but they emailed me an invoice for the replacement. But after exchanging a couple of text messages, that got cleared up before I picked up the car.
Since then the car has been driven in the rain and been washed a couple of times. No leaks.
Overall, it was an appropriate, satisfactory ending. However, Tesla needs to do something about their automatic invoicing.