[Jakey]

From what I understand (which could easily be wrong): the algorithms the stock ECU uses to "run" your engine based off of the OEM timing and fuel maps can not compensate for the increase in air and fuel you are seeing due to the modifications. By having a custom chip burnt, the timing and fuel maps are adjusted to compensate for the increase in air and fuel which allows the ECU's algorithms to properly "run" your engine (within reason).