piston in the ports doesnt matter.
its the point at which the piston opens the port that matters as this governs your port timing or duration.
if you try spacing your cylinder up 1mm to get the bottom of the ports level with the piston at bdc (which doesnt matter at all) as a side effect for every mm you raise the cylinder you raise the peak power by about 1500 -2000 rpm. obviously depending on stroke and current port height.
aim for duration ie port opening first. some manufacturers ie Husqvarna design their pistons at bdc to be ABOVE the bottom of the ports.
its sometimes beneficial to have the piston above so dont worry. but what is critically important is your duration and the point of opening .
dont take my word for it. google it.