That is exactly what happened in the Metacritic POTY, they mention Flight Simulator by name, so it was definitely counted (and so were the Director's Cut games from Sony).
Understand what? All I said is that Flight Simulator was computed as a 90+ game for MS so we can assume that any game releasing on a new platform will count for any other publisher (the same happened to Sony re-releases last year). Neither Sony or MS would've even been eligible for the award if games releasing in a new platform or re-releases were not considered.