Thats not strictly true: MANY problems can happen that are not obviously caused by either hardware or software.
If your screen turns yellow in one corner and smoke comes out, thats obviously hardware. If you update to a new OS and email stops working, then it comes back when you downgrade, thats obviously software. Most problems are in the middle. GPS sometimes shuts off? Is that hardware or software? How about an increase in app crashes? It takes time (= money) to diagnose many problems. If youve complicated your system with software mods that are known to cause problems for some (even many) people, then that makes it hard for Apple to judge, is this our software failing, or bad hardware? It could in fact, be YOUR software thats failing.
So Apple has said jailbreaking CAN (not WILL, but CAN) interfere with your warranty.
Solution: reverse the jailbreak. Restore your phone to original state, and see if the problem still exists. Thats standard procedure anyway, so its really not too much to ask. And if you do that, Apple will never know you had modded your OS, and it wont come back to bite you.
(Bold added.) Apple has said exactly what you said. What exactly is your disagreement with Apples statements today? What do they not get? by saying that jailbreak-related problems may be your own responsibility to fix?