I'm not sure the dealer would be willing to refund you for the factory sound system because the residual value of the factory sound system is almost certainly miniscule compared to the cost of labor involved in removing it.
Why is the residual value so small? Lack of standardization. A lot of automakers use their own mounting system for the head unit, which means if I bought a Lexus and asked the dealer to take out the head unit, the dealer wouldn't be able to turn around and sell it to somebody who wanted a better unit in their Ford. It goes beyond the mounting system though.
A lot of automakers have their own plug and wiring standards too. If you buy an aftermarket head unit, you usually get a pigtail that plugs into it with unterminated wires on the other side. Then you buy a wiring harness kit specific to your car which has unterminated wires running into a plug that connects to the vehicle harness. Soldering ensues (or wire nuts or electrical tape for the lazy...). Since the aftermarket does have a strong incentive to standardize, the wires on the pigtail that come with the head unit match the colors of the wires in the harness kit, which actually make the process pretty straightforward if you're even halfway handy.
What all of that means is that the unit out of your hypothetical Lexus (which doesn't come with a pigtail with unterminated wires) is going to be hell to get working in somebody else's Ford. Between the physical and electrical incompatibility, the residual value of a head unit has to be pretty close to zero for anybody who doesn't own basically the same car.