Just an update: I got the truck back from the dealer, and they rushed on the job....
When installing the B pillar trim on the driver's side, they covered up the seat belt...so that was comical, they fixed that before I could leave.
So the next day, I notice the sunshade is very floppy, took me a bit but I figured out it was not in the guides, took me some time but I was actually able to fix it.
The next thing I notice is that the rear portion seems loose/not very tight, could not quite figure out if it was me just imagining it, then I found two bolts in the cup holder......so I think they forgot to install the rear bolts.
Also, the glass alignment is not great, not horrible but it could be better and now I see how it is installed, I think I can easily adjust it.
Very interesting turn of events for sure. At this point, I may never open the sunroof again!