I suspect it's similar to the reasons why many wireless drivers require binary blobs (either firmware, or the entire driver) -- you can change the software to let you operate outside of the limits allowed by federal regulators, because those limits are enforced in software.
Same goes for the physical breaks on the car. If someone install custom breaks on their cars that is found to be unsafe, it is illegal. This doesn't however make installing custom breaks on your car illegal. On the opposite, the law explicitly allows you to do so, and enforces the car manufacturers to give you documentation so you can do it.
Why should federal regulators differential between someone installing custom physical breaks on your car, or someone installing custom software that controls the breaks. Whats the difference?
