As long as the instaler has some experiance, it isn't a problem. Not to mention most of your high end car alarms (like clifford) come with a preout and is designed to arm and disarm the stock system as required. In fact I am having a clifford put in my 2005 accord coupe.
can you tell me then, are cliffords better than vipers? or are both about the same? Also if a get the remote starter will it mess up the security in the starter that has to do with the chip in the key?