I don't think modifying the software on the iPhone breaks the warranty, a hardware modification, or cracking the case open would be different.
Compare it to a Macbook, etc..you can load XP, or Vista, not supported, but does not void the warranty.
Hmm...makes me think....Bootcamp for iPhone?
The only other thing you would have to be careful of would be modifying a file that would alter the operation of the hardware, (ie boost signal) then you might have to worry about the FCC.
my .02 cents.