What you’re paying more for is the separate clear coat step. My dad went with the cheaper package and complained that the integrated clear coat does not shine like he expected a new paint job should. It also seemed to scratch easily and show rub marks after automatic car wash.
This tech board has a bit more info on the difference.

Indeed the urethane clear coat is what you pay for. A clear coat is the most important part of a paint job, it’s what gives the paint its shine, better scratch protection and UV protection. Your car sits in the sun all day, and without a quality clear coat the paint will be affected much faster by exposure. Make no mistake, car wash brushes WILL mark even the best of clearcoat, it’s inevitable… The quality of the paint also affects the price. Urethane paint comes in many grades or qualities, ranging from cheap hardware store paint to high quality custom paint, which can easily cost over 100$/pint. For example I often paint motorcycle tanks and tins with a custom urethane paint, which costs about 80$/pint depending on the color, add to this the price of the reducer, plus the primer/hardener/reducer before painting, and then the clearcoat/hardener/reducer…well you get the picture.

As for the prices you put in your question, I think you should consider the car. Is it an every day car, or a prized classic/sports car? For a regular car 1000$ seems fair to me. If it’s a really valuable vehicle I would charge much more since top quality urathane would be used.

Oh, and make sure they do use primer before painting, as it’s not mentionned in your post. Cheers!

Ultimate is how the job is supposed to be done. The other option is the industry shortcut used to make an extra buck when doing rehab for insurance funding. Don’t pick that one.