... about 75% of car dealerships are owned by and staffed by, in about equal proportions, incompetents and people of questionable character.
I hate going to car lots - it's a very rare thing to ever find anyone honest. I have on occasion, but the experience normally starts with the greasy pointy shoed sales type who comes out with some lame line like he's trying to win the worst pickup line contest in a bar, and then continues on with equally questionable people in every other department trying to extract every last cent of your hard earned money.
My latest foray was picking up my Rubicon ... they kept me there for four hours and then decided a scratch on the black fender was no big deal and I should get over it. I managed to get a document saying they'd try to buff it out. Weeks before there was paint missing on an $80k truck when we picked it up. How does the detailing guy miss 6" of missing paint on a fender? (they fixed that, thankfully).
Rest assured I will never set foot in the place again. That's the ultimate victory for me.
I guess you could just continue to beat your head against the wall and keep bothering the GM to look for your windows because since you didn't get them, they must still be there, or you could buy aftermarket windows, or pay the dealer wholesale and then tell them in a very loud tone when there are a bunch of customers around, that it's the last time they'll get the satisfaction of your business and never set foot in the place again, and tell everyone who asks what types they were - maybe you'll cost them a sale or ten.
Take solace in the fact that you've made a lot of people here aware of what is supposed to be in their Jeep at delivery.
No offence to any actual honest dealerships on here. An honest one would have had a delivery slip and gone through everything with the OP when he picked his jeep up. A really superlative one would have removed the soft top from under the hard top and asked the customer which one they wanted to drive away with (and delivered the other one). They might actually earn their PDI charges that way.