The order the pistons move up and down in is the same from tdc compresion stroke to tdc exhaughst stoke. You can time the bottom end to comparitively to the cam in either position and it will run fine as it is actually the cam timing which determines valve movment in relation to tdc on no1. What you cant do is set the ignition timing 180 degrees out from valve timing and expect any results as the cylinder will not build pressure to fire.