I hope I can put together a coherent post with an answer to this question and address some of the other charges and counter-charges.
The simple answer is that Churches aren't formed by self-evident truths which say: "I like Reformed Baptist theology but believe a Presbyterian government would be good too."
History matters. Confessions matter. The way that Churches form historically and the resources a present Christian reaches back toward matter in sustaining not merely the individual believer but the larger Church as well.
This article may seem out of place but it's important as to why Presbyterians have retained Ruling Elders for centuries, but congregational churches ended up abandoning the office for some time.
by Iain MurrayI have often put off taking up this subject and I do so now with considerable hesitation. (footnotes 1, 2) The reason why I have this feeling is that I would much prefer to speak on a subject upon which I have more confidence and certainty. The truth is that I once had a good deal...
housechurch.org
This is going to sound pejorative, but a present Reformed Baptist Church, established in the last couple of years or decades, can scarcely be called "historical" simply because the particular congregation adopts a Confession from the 17th Century. I realize there are some centuries-old congregations that have maintained their Confession of the 1689 and I would consider that to be historical in a general sense.
The reason I don't consider the former historical is because a Church is not really in the stream of anything that binds them as long as it is merely held by a particular congregation that hasn't survived generations of trials.
It's easy to point to Presbyterian Churches as unfaithful because one only needs to point at multiple unfaithful congregations in a massive body and compare a single congregation in a Baptist Church as note how faithful that Baptist Church presently is.
I suppose the point I'm making is that you have to have some foundation to build upon for a Church. The PCA, for all its faults, didn't spring up from nothing. It came from a Presbyterian tradition and separated in order to remain faithful to the Great Commission and the Reformed Faith. We have polemical battles all the time within the Church and the consistent "pull" is that our Constitution is the Westminster Standards as well as a long tradition of a form of Church Order that provides for the functioning of a Presbyterian form of government.
What resources would a group of Baptists who "like" Presbyterian government reach for? I don't think people realize how hard it is to fight for Presbyterianism. It's exhausting and frustrating and glorious all at the same time.
To be Presbyterian is, to some extent, being committed to the idea that another minister or elder in error (or his Church) is still part of your Church even when in grave error, and you have to do more than just wash your hands of them without process or because you're convinced that as long as my local congregation is faithful, then it's easy to maintain the faith. When you have to engage in theological argument with other Elders at Presbytery or GA, however, you realize how easy it is to convince a small congregation (or just yourself) and how much work it takes to convince others. The thing that keeps the Presbyterian committed, even as he loses some battles, is that he is committed to a Confession that he thinks is Biblical. Without that Confession, and the line of history behind it, there's just nothing that would sustain a man under those circumstances.
I guess what I'm saying, ultimately, is that enduring institutions are not ultimately formed without some history behind them. I don't wish this upon any Reformed Baptist Churches but the history of congregations even maintaining a plurality of elders isn't good. Presbyterianism variously waxes and wanes in history, but there is a heritage in the sense that our Standards are continuously practiced and thought about (and include more than a Confession but the additional resources in the catechisms) and we have a Book of Church Order that has elements that go back centuries. That's why, even if local congregations and Presbyteries apostatize, there are always Presbyterian bodies that pick up where the others left off.