Hard to tell if the flywheel center is exactly on the center of the piston bore, but that's where I would put it (or leave it), just for the purposes of maintaining geometric concentricity with all of the moving parts involved, whether elliptical, linear or rotational, thus reducing inertial imbalance which could result in vibrations which could become resonant if the rotational frequency should approach the natural deflection frequency of the support beam. Also, keep the stationary parts out of the way of the moving parts.