Capone was essentially finished as Outfit boss when he went away on the double-digit-sentence tax rap. None of his biographers (and he's had two excellent ones) has said he exerted any control over the Outfit while he was away. In fact, Alcatraz was designed, in part to completely isolate the most high-powered criminals from their associates--only Capone's immediate family was cleared to visit him.

As for the Commission: One of Charlie Luciano's most brilliant moves was to name Capone (rather than himself) as "chairman." He did it to bring the Outfit into the Commission even though it wasn't an official Mafia family at the time. He also did it to try to curb some of the Outfit's most blatant excesses. The St. Valentine's Day massacre, for example, brought unwanted heat down on the Mob, and Luciano wanted to prevent any further missteps. Luciano also named Bonanno as "secretary" of the Commission--an attempt to bring the old-line Sicilians around to supporting his view of accepting non-Sicilians (and even non-Italians) if they could be helpful.