I'm not really convinced by this as a problem: it should be easy to keep both sides (lawyers and programmers) happy. For example, only updating the software by plugging in a USB key; keeping the USB socket under a cover with some kind of awkward screwdriver (eg pentalobe), and then breaking a paper label that would denote the warranty is void.
i.e. Users should be free to modify their device's software, but with some clear restriction to "experts only, at your own risk" would be a reasonable balance.
As for "(and in most automotive architectures they are not fully isolated)", that sounds to me completely crazy. I don't think that feeding a music player with a malicious file should ever be able, even in theory, to interfere with the brakes!