The physical good that software is distributed on is covered by the first-sale doctrine and you can resell that, but it won't do much good because you can't reassign your license to it. If I have a license for Windows but lose the physical disc, I can buy your disc. However, without owning a license, I wouldn't have the right to use the software.
If the SCOTUS upholds the circuit court's decision, I wouldn't be able to buy your Windows disc anymore (assuming it's pressed outside of the US).
Of course, this only works for really expensive but limited edition cars. If there is a several year waiting list just to get the chance to drop half a million on a car, the car maker can get away with almost anything--the customer is obviously willing to go through a lot of trouble! This is designed to stop people from flipping supercars.
Also, there is a very important difference between a voluntary contract and an abuse of copyright law. Now, if every car maker mandated such a contract on every car, it would be a big issue even if it was ostensibly voluntary. In a free market, some other company not mandating such a contract would emerge; however, markets rarely function perfectly. I think this is an interesting parallel to the whole safe boot nonsense: if there was more diversity in the market it wouldn't be an issue, but the market is heavily dominated by a handful of companies, so it is an issue from a purely practical standpoint.
And while they couldn't ban after market parts, they could make the engine not start if the new brakes/mufflers/cat didn't give the correct crypto response to the engine management system.
And just imagine that congress would bow down to the car makers (that it had just bailed out) and rule that you couldn't modify the engine computer - in the interests of safety of course.
Of course, I'm not an expert, and could certainly be missing information on other components of the GT-R. Either way, it's useful to keep in mind that the GT-R is a really crazy car :P.
Ford is more likely to suffer from the anger of departing new buyers than gain from there not being 40year old Ford pickups rusting in fields.
Microsoft has already won a number of cases stopping companies selling unused software licenses. This is actually a big deal if you are a company - if you have $$$$ in MSFT licenses that you have been treating as assets and the court rules that they can't be sold and so have zero value - you might have a lot of auditors and shareholders you have lied to.