The full throttle height is function of pressure altitude as seen directly from altimeter, given the altimeter base level setting. Supercharger increases manifold pressure and that ability depends on outside pressure and dynamic pressure on intake regardless density of the outside air. Air density is, of course, funtion of pressure and temperature but supercharger only sees the pressure.
BTW Gaming wise it's more important that the relative performance of the planes is about right and that is pretty easy to test regardless atmospheric model of the game, given that all the planes can be tested in the same conditions.
BTW2 I just looked in my crystal ball a saw that soon my sayings will be denied and scans from various books will be posted with thick, red underlinings