I figure that the Senate Committee used the info given them by Willie Cicci and Frankie 5 Angels to make that (Family) chart. Cicci, as a mere button, probably didn't know the true hierarchy (remember, there were a lot of buffers) and even though Pentangeli was at least a capo, and should have known his immediate "superior", he may have been left in the dark intentionally since it appears Mike was concentrating his Family's efforts in Nevada, and probably somewhat forgetting about the New York faction.

In any event, I believe Turnbull's suggestion about Mike keeping things close to his vest sums it up best (there probably wasn't an underboss).