The third wing
The reformers are called magisterial because they worked with magistrates. On the other side of that contrast stood the Anabaptists, who paid for it, and the 1689 Confession does not descend from them.
The documents behind this page: the Schleitheim Articles of 1527, the Zurich council's sentence on Felix Manz, the Diet of Speyer in 1529, Thomas Helwys in 1612, and the London Confession of 1644.
That the Baptist line runs back to Zurich in 1525.
The central practice is the same, believers' baptism on profession of faith. Both groups were called Anabaptists by their enemies and both denied the name. And there is a real thread: John Smyth's English exiles in Amsterdam were in contact with the Waterlander Mennonites from 1609, and Smyth eventually sought union with them. Anyone who says the two stories touch is right.
They touch in the General Baptist line, not in the Particular Baptist one. The two were separate English movements: the General Baptists held that Christ died for all, the Particular Baptists that he died for the elect. The Particular Baptists, who wrote the 1689 Confession, came out of the Jacob-Lathrop-Jessey Separatist congregation in London between 1638 and 1641, which is English Puritanism. They said so themselves: the 1644 London Confession's title page calls them commonly, though falsely, called Anabaptists. The 1689 then follows Westminster and Savoy chapter by chapter wherever it agrees. They shared the practice. On ancestry the Particular Baptist line runs through English Separatism rather than the continent, and on soteriology the two movements differed.
That the Reformation's violence was Rome's doing.
The Reformation's violence runs through Protestant hands. Felix Manz was drowned in the Limmat on 5 January 1527 by order of the Zurich council, in the city Zwingli was reforming: a Protestant government executing a Protestant over baptism, by a method chosen to mock the baptism he died for. In 1529 the Diet of Speyer made re-baptism a capital offence across the empire, and Catholic and Lutheran estates agreed on it. The men praised for recovering the gospel are the same men.
The Schleitheim Articles of 1527 had already put the answer in writing, three months before their author was executed: the church is gathered by confession and the sword belongs outside it. Reformed churches reached the same position later, and paid nothing for it. It was available in 1527, in print, from people who paid for holding it.
That the Anabaptists were violent revolutionaries.
Munster happened. Between 1534 and 1535 an apocalyptic faction seized the city, declared it the New Jerusalem, expelled or forcibly baptised those who would not join, instituted polygamy, and killed dissenters. The siege that ended it was brutal in turn. Anyone defending the movement has to carry this.
It was one city over eighteen months, and the movement before and after it was overwhelmingly non-violent. Schleitheim had renounced the sword seven years earlier, and Menno Simons gathered the survivors on that basis from 1536. What Munster mainly did was give every authority in Europe a reason to treat every Anabaptist as a threat, which is why the name became an accusation.
That American religious liberty descends from them.
They went further than the 1689 Second London Baptist Confession does, so a church confessing it cannot adopt the Schleitheim position without contradicting its own chapter 24. The Schleitheim position was separation: many refused oaths, refused civil office, and refused the sword outright. The 1689 Confession says the opposite in 24.2, that Christians may hold the magistrate's office and may wage war on just and necessary occasions. Admiring their answer on conscience does not mean taking their answer on the state.
On liberty of conscience they were early, and the clearest early English statement is Helwys in 1612. Thomas Helwys published in 1612 that the king has no authority over conscience, naming heretics, Turks and Jews as covered by it, and died in prison. That is a fuller claim than most of Europe would make for another century and a half.