I agree that they probably just misplaced it. Push back on them and keep making noise until you get what you paid for. Its probably not them being malicious, more likely just incompetence.
I have the same one they're advertising and its working great for me. I had gorilla glass back when I had a wrangler, and it was just as prone to chips as the normal glass. Eventually I gave up and put a normal windshield in since it wasn't worth paying twice as much for a windshield.
What I wish I had bought before delivery was a windshield protection kit. I broke my windshield within a few months of delivery and it was a pain to get a replacement. I installed the film onto my new windshield, but wish I had just done it from the beginning. I used this one...
Film was my first mods as well:
windshield protection film as a diy kit
tint all around
partial PPF
Your insurance won't replace the tint on your windshield, so I recommend putting windshield protection film on, so you're not needing to replace it if you break your windshield.
I assume you have a soft top? I'd just bring it back to the dealership and let them sort it out under warranty. I wouldn't want to wait to figure it out myself, water getting into the wrong places could damage other things while you wait.
3 weeks isn't too bad. It took me over double that to get my new windshield when I broke it after a few thousand miles. I put the grab gard film kit onto my new one to hopefully not go through that fiasco again. I'm glad I did, because I've had a few hard hits since then and the film kept the...
This is the one I put onto my second windshield after my first windshield broke: https://www.grab-gard.com/products/ford-bronco-windshield-protection-kit
It's been good, was easy to install.