Yes, the manufacturer cannot set the dealership price, just the MSRP. They can set franchise agreements and guidelines. They are supposed to honor order price (we looked up the Michigan laws yesterday, actually). The part that people are upset about is exactly what you described. Reserving a vehicle for the $100, the dealership asking for more then finally getting the vehicle delivered and getting some BS market adjustment or added "dealer installed" items. I saw quite a few dealerships charging $200-500 for wheel locks...... they are $50 retail. The dealerships then tell you that you have 48 hrs to take delivery or lose your order.
My specific Bronco order (from almost 2 years ago) was the$100 online deposit, set the dealership you want to take delivery at. I get an email saying I need to come in to pick my options in 3 days or lose my reservation. I get there and they want another $400 non-refundable deposit made to the dealership plus they wanted to run my credit check. After I explained that running a credit check was idiotic because the vehicle was a year away from delivery, I paid the $400 so I wouldn't lose my order. If I gave my order up, the dealership still gets that vehicle allocation. From what I saw on some other forums, dealers were asking $3-5k deposits. The whole experience from all manufacturers is poor.