One reason why the local churches cannot be completely autonomous, is that the teachings of the Church --- that is to say, not opinions of this or that cleric, this or that theologian, but the officiai doctrines -- are authoritative; if they were not, Christ would not have told us to resolve conflicts among the brothers by listening to the Church.
You posit that "the churches cannot be autonomous, ... because the official doctrines of a larger assembly are authoritative."
Then you bring up local church discipline.
Local assemblies *following God's Word* in matters of church discipline need no Roman hierarchy to carry out the Word of God.
I've witnessed successful churches do this in person over (too many) decades.
In practice, very few churches are in isolation. Most belong to a fellowship of like-minded churches, who share a common doctrinal statement that each adheres to locally.
Historically, that's the reason there have been Councils, the prototype being the one in Jerusalem, so they'd all be in one Body, with one Head, led by the same Holy Spirit.