We still live in a compromised situation and we have lots of legacy issues regarding church structures. It is not the will of God to bring down everything quickly because leadership is important and leaders of smaller congregations do well to have accountability to other ministers.

In the ideal world, all what we call "pastors" in a city really are the "elders" of the city. They should have fellowship with one another, proving their ability to love one another even when they don't agree on all things. But many times there is strife between pastors so they don't relate properly. There is a need for humility and following the Spirit's leadership to establish righteous relationships and deal with hurts and misunderstandings.

There is also a role for pioneers of church movements whom we might call apostles. God will raise up apostles to pioneer new churches when He wants to. These apostles are not like the 12 apostles of the lamb, they are basically gifted church planters with a commission from the Lord to start new churches. Its important to be sure of the calling of the Lord to start a church, as opposed to joining an existing one.

An "apostle" who starts a church and raises up leaders to care for it after he moves on could have authority to speak into the leadership of that church after he leaves, it depends on the arrangement or understanding that was come to before he handed on leadership.

So whether the churches are autonomous after the founder leaves depends on the agreement that those in question had in the presence of God before the handover of operational authority happened.

Clearly Paul claimed some authority over the churches he started, like the one at Corinth. But Paul had a hard time assering his authority there. It wasn't a dictatorial authority, but more a fatherly authority.

A lot more study could go into this. But the difficulty we have is this: we are not working with a clean slate. All kinds of churches and structures are on the map, and it would be presumptuous to demand that in your timing or mine these churches radically change their leadership structure to accommodate some kind of idealistic church government structure.