Yes, it should be pretty clear that Frankie succeeded Clemenza as Corleone Don (he succeeded Michael). I think what is confusing Enzo is that Mike, although not directly running a NY style family out in Nevada, still has as much influence and control over the Corleone family as he wants to have. Another thing is that FFC took a few liberties with the organization of the Mafia by having Michael conducting business way out in Nevada. His doing so parallels somewhat Joe Bonanno and Tony Accardo (Chicago) who, though both were "retired", still got command responses from their respective family members when they chose to exercise that command.

By the way, I just watched GFII a few hours ago and reviewed the novel. In neither did I detect that Michael was uneasy or unsure at the funeral or in his novel conversation with Tom. In fact, in that conversation he states that the Corleone family is alot stronger than anyone thinks.