Sorry about the bike, buying a new bike should be a fun experience. That said, I think a 60 mm stem will be too short. So if that is what it takes to fit the bike, get a different bike.

If you are unhappy, the shop should do whatever they can to make you happy, either fit you correctly on the bike you have, order the smaller size, or accept the bike as a return. If you return the bike they might screw you over with a store credit, but you could call your credit card company and I'm sure you would prevail.

I'm a Trek fan, and the new Madones are wonderful. It's no surprise you liked the ride. Frame technology and the best warranty in the business make Trek a great value. I'm not sure which Trek you were looking at (4.5, 4.7, 5.1), but you should be able to buy a 5.1 WSD for under $2700, with basically full Ultegra, US built frame and all the new tech.

Best of luck, and do what feels best!