The stock code contains a feature which has been nicknamed the "octane value." Basically, the if the ECU sees a knock sum over 5, it reduces the maximum amount of timing advance you can have. It saves this in long term memory, and it can only go away of you have less than 3 knock sum, in which case it will taper away slowly.
If you use good gas and keep track of what it happening with the car, then there is no reason to keep this feature. It is mainly designed as a protection against something happening to the car (such as using 87 octane fuel, or something breaking) so that the ECU can reduce the timing level to help keep stuff from blowing up. All TMO chips set the octane to the maximum possible each time you started the car, this code just goes a step beyond that and gives you maximum octane all the time.