This. Toyota doesn't want to be responsible if some third party garage or vehicle owner hacks the braking software and causes a car not to stop at a stop light resulting in a multi-car pile up.
Change the brakes, struts, suspension, transmission etc etc - fine. Hack the software to make it perform some trick? No thanks.
Take the simple example of vehicles with in-dash displays. By law if you have a DVD player manufacturers are not allowed to have the video show unless the car is in park (or maybe the engine is off?). There are guides around to modify this behaviour so that you can watch the DVD while the car is driving.
Sounds harmless enough. Suppose this has an effect on the number of fatal injuries in that particular brand of car (hypothetically speaking).
Now all of a sudden, brand X has been damaged because the stats only show that drivers of brand X vehicle are more likely to die in a car accident. There is no way to pick apart those statistics to understand that it was due to a vehicle modification.
Once you get into more critical components the effect would likely be more pronounced.