How does transforming points with a transformMatrix work in fabricJS?

Not really a geometric problem.
The geometric part was solve by you. If you would look at internal polygon class from fabricjs you would notice that polygon as a calcDimension function where every point gets an offset:
http://fabricjs.com/docs/fabric.Polygon.html

To calculate canvas position you have to add that offset back before transforming.

var canvas = new fabric.Canvas("c", {selection: false});

var polygon = new fabric.Polygon([
  new fabric.Point(200, 50),
  new fabric.Point(250, 150),
  new fabric.Point(150, 150)
]);

polygon.on("modified", function () {
  var matrix = this.calcTransformMatrix();
  var transformedPoints = this.get("points")
  .map(function(p){
    return new fabric.Point(p.x - polygon.minX -polygon.width/2, p.y - polygon.minY - polygon.height/2);
    })
  .map(function(p){
    return fabric.util.transformPoint(p, matrix);
  });
  var circles = transformedPoints.map(function(p){
    return new fabric.Circle({
      left: p.x,
      top: p.y,
      radius: 3,
      fill: "red",
      originX: "center",
      originY: "center",
      hasControls: false,
      hasBorders: false,
      selectable: false
    });
  });
  
  this.canvas.clear().add(this).add.apply(this.canvas, circles).setActiveObject(this).renderAll();
});

canvas.add(polygon).renderAll();
canvas {
  border: 1px solid;
}
<script src="https://cdnjs.cloudflare.com/ajax/libs/fabric.js/1.6.3/fabric.js"></script>
<p>
Move, scale and rotate the polygon. The three red dots should match with the corners of the polygon after each modification.
</p>
<canvas id="c" width="600" height="400"></canvas>

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