I line up the prop at 3 oclock when the piston is on compression...on all engines no matter what position the engine is mounted....vertically or horizontally mounted engines. This is the best method for easy starting and keeping the prop from getting broken on a bad dead-stick landing. I can think of absolutely no reason to mount the prop inline with the piston....unless of course this makes the prop line up at 3 oclock on compression. A balanced prop cannot influence how the engine runs depending upon the mounting position of the prop. There is no mysterious force between the prop and the piston that needs alignment.