Well, the AFC isn't going to affect timing as much if you are starting with a flashed ECU since the corrections are going to be less. But the point of the flash is to get the timing where it needs to be and then the AFC should be used just to fine tune the fueling. If there isn't good timing with the flash, then the flash needs work. But even if timing doesn't move, there is power to had from a flashed ECU by leaning out the mixture to something more reasonable than the typical mail-in flash.