The big "got ya
" is if it's anything that could be software related. Reception for example, they could say it's because it is or has been rooted. Then it would be up to you to prove the same condition would still exist had it not ever been rooted.
They could say because you were rooted malware (or whatever they wanted to say it was) caused your radio to not work correctly and it would cost X amount of dollars to replace your phone of have Motorola do a complete wipe to repair the effected software.
If it's a hardware failure they could say something caused your phone to overclock while it was rooted thereby voiding the warranty.
I'm not saying they are going to do this for now but you know it's coming down the road. They may say they included the ability to check it to help the consumer but you know at some point it will be used against us, this kind of stuff always is.