What you wish to “reconcile” is not in conflict. Don’t confuse the Kingodm of which Jesus speaks (namely the Kingdom of Heaven) with the governance of the Church. Although the Church is part of the Kingdom of Heaven, its governance is not.
Nothing about Church governance was instituted by Our Lord. Jesus gave us basic leadership (bishops and Popes) but He did not tell us how those leaders were to organize or exercise their authority (Jesus did not establish such a thing as a Cardinal or the College of Cardinals or Papal nuncios or any other such things).
As such, the governing structure of the Church is finite and subject to change. It is a purely human invention (and no theologian clamis otherwise) and is thus, by definition, of this world. From time to time, different leaders have organized and administered their authority differently as they see fit according to the circumstances of their time, which is their right and duty.