It's pretty hard to imagine an app so powerful that it not only bypasses Apple's sandbox, but it even goes on to damage the device's internals. If such an app could exist, it would exist right now.Just because they can doesn't mean they should. They already have tons of customers that go in for "fixes" because they barely understand how to use their devices as is. Now add to that the "I know better than Apple" idiots? Good luck making an appointment for something that truly went wrong with a device for a legit reason. Yeah, I get the people that are "my device, my choice" blah, blah, blah. Those same people are the first in line to blame Apple for something they themselves screwed up and want Apple to fix it free of charge.
That means your comment refers to one of two things:
1. You're talking about software issues. Good news! Those aren't covered by warranties (in the traditional sense) so nothing is gained and nothing is lost.
2. You're talking about hardware issues. Those are and will continue to be covered by warranties and AppleCare and such, provided they're accidental and not caused by the user (perforce by mishandling the device, according to the above). So, nothing is different from now.
Besides, Apple's tech support doesn't really care about the software installed, as proven by the countless reports of people who got their phones repaired (for hardware issues) after jailbreaking.