Carlo Gambino wasn´t made the official boss until 1960. During the years between 1957 and 1960 he served as the acting boss. You can find this in FBI documents on the Mary Farrell Foundation site. As an acting boss, Gambino could not not have controlled the Commission.
After the murder of Anastasia, the family was divided and Gambino was given the task by the Commission to restore order in the Family. In 1960, the Family elected Gambino the official boss.

Guys, I´m sorry to say it, but you are relying too much on Wikipedia. Using Wikipedia is easy and accessible, but extremely unreliable when it comes to sharing knowledge on the Mafia. But you have to dig a lot deeper in order to come closer to the truth. No boss was ever a boss of bosses after the creation of the Commission. Not even technically speaking. Having a boss of bosses on the Commission would undermine the purpose and functions of it. It´s two completely different systems of rule that can never be combined. All Families, especially those on the Commission, was autonomous. All bosses on there ruled their own Families and to allow somebody else to exert pressure or secretly control your Family would be a sign of weakness and a sure way to lose face.
When the Bonanno Family lost its seat on the Commission, perhaps as early as 1975 when Rastelli was sent away, it looks like the Family was governed by the Commission. I can´t think of any other cases where sitting Families on the Commission were controlled by it. Can you?