Not defending the dealer but a couple thoughts. The labor is an estimate so they should only bill you for what was actually done on the glass cleanup. Having done it myself in the past, it can be more complicated than one might think and the bulk of the work is not the cabin but inside the door itself.
The window shatters and unfortunatley lots of small pieces of the safety glass fall into every nook and cranny of the door and then a bunch pools up at the bottom. If you don't get all of them out then there will be a permanent rattle for the rest of the usefull life of the vehicle. Sadly, the door is often poorly designed by some vendors and there aren't any drain holes big enough to clean out the glass. So you are limited to vacuuming from the top in an area where it is hard to get a lot of suction.
Perhaps someone in this forum has already taken apart the LC door and can comment on the drain hole design issue. Hopefully Toyota did it right. I wouldn't take it lightly and would put more emphasis on the dealer to do a thorough job rather than saving an hour or two of labor. Otherwise, you could end up with an extra percussion section in the car as you drive down the road.
