Oh, that is really bad. Hope they pay the new windshield. If they couldn't get the upper part of the windshield into the frame in the body. Then they probably didn't center it well before pulling the rope in the rubber seal from inside the car.
Its important to find a glass shop with long experience. At best an old person who have mounted many windshield in (now) vintage cars. Modern cars with glued screen are completely different, and most modern shops only have experience in these kind of jobs and to repair small chips in the glass from gravel.
Was the new windshield seal stiff?
Also. When you write "silicone" I hope you mean some polyurethane sealant or equivalent. Because there are many reasons not to use silicone products on cars (trouble when doing paint jobs, alot of them develope acid when hardening wich can cause rust etc.).
w460.333 1982 Colorado Beige