It is their product. They can put whatever restrictions on it they want. Ferrari could say that they will not allow anyone to modify their cars, but they have no way of stopping people, so they don't restrict it.
... they do try, though. Ferrari get very upset when a tuner modifies one of their cars. They don't like it and insist that the Tuner removes all Ferrari badges and that the car is not called or marketed as a Ferrari. This might legally be the strongest action they can take to prevent changes to what is someone else's property. You'll never see a Ferrari badge on a Koenig Competition, for instance. I think it's just Ferrari's way of trying to control their public image.
I can't say though how they would react to someone privately modifying their Ferrari. Also, there are plenty of 365GTB/4s running around with their roofs chopped off to turn them into GTS/4 replicas, and all of these that I have seen still have a Ferrari badge.
They have also put restrictions in the sales contract on various cars.. I remember reading that buyers of the F50 had to agree never to lend their car to a magazine for the purpose of being compared to a McLaren F1. I also read more recently that buyers of the Enzo cannot sell the car for a rather long time. Don't know how true this is as I am sure I've seen used examples on Auto Trader. I also don't know how much Ferrari can really do should an owner choose to breach either of these terms, apart perhaps from not invite said owner to purchase the next limited edition supercar.
Ultimately, though, and this is the same for computer games like GT4, Ferrari still own the intellectual rights or copyright to the car that they sell you even if you own the car itself, and these prevent individuals from making copies of this car. So while you own the GT4 disc and packaging that you purchased, PD still have copyright on the code. Again, like with Ferrari, this may give PD strong legal ground to prevent unauthorised manufacture of copies, but maybe weaker ground to preven modifications to the code / mechanics / appearance. I dunno though, I'm just guessing.
