Metrolinx are just only following the individual plans of each system, even though it is supposed to be the regional planning body. Metrolinx are just tools.
Metrolinx is bound by law to conform to municipalities' plans. In reality it should be the other way around, but you know how governments react when their existing powers are threatened. McGuinty et al just didn't have the courage to write into the law regional powers for Metrolinx.