I'm not clear on what you mean here. There is one section of the bottom edge of the piston that runs past the intake port when it is at the top of the stroke. If that section has been damaged, it won't open and close the port cleanly and the engine may not run as well as usual due to having the wrong port timing. For the other three quarters of the piston's circumference, it is only important to have a good fit so that the piston can't wobble, or scratch against the bore. Are you saying that when the piston is at the top of the stroke, the bottom of the piston is going past the exhaust port? You'd have pretty serious damage for that to happen. The engine can't run properly, and may not run at all, if the exhaust port is partly open to the crankcase at the top of the stroke.
