This is more like you replaced the exhaust system with something bought 3rd and reflashed your car with a 3rd party CAN bus widget, then complain when it overheats and has a flat zone around 3500 rpm.
Jailbreaking isn't like opening the hood, it's effectively messing with the system and setup (just like the ECU example). It might not cause any problems, but it also might.
I have no problem with that by the way, but you are on your own lookout and should accept it as part of the deal. Similarly if I damage engine performance due to bad tuning it's my problem, not theirs.
I do think it's too broad of manufacturers (whether car or phone) to apply a blanket warranty denial in such cases. But in the phone case, no reason apple should accept bug reports on a jailbroken system if it can't be reproduced on a "stock" one.
