I'm saying buy a different tailgate with the window already in it and respray that panel alone lol.

Um...dude, if it isn't how you want it then go back and tell them to fix it no matter how hard it is. it's not your problem Just make sure they know that you (and all the forum members here) remember faces and important things, such as the guarantee of a window seal. If you hassle them into getting it done properly and then a problem comes along, you will have backup.