ExtrudeGeometry makes a hard presumption that the shape to be extruded is defined in the xy plane and that the extrusion is to be along +z. See, for example, lines 421-449 of the source code, in particular line 432:

v( vert.x, vert.y, depth / steps * s );

Where v(x, y, z) is a member function that pushes a coordinate triple into the object's vertex array; vert.x and vert.y are the x- and y-coordinates of the shape being extruded; and depth / steps * s yields the z-coordinate of the extrusion at a particular step.

Furthermore, the presumption about the shape being in the xy plane is necessary because Shape objects are two-dimensional; the Flatland of the xy plane is the only world they know.

To get the behavior you want (i.e., without rotations), you would have to implement it yourself. You could start from what ExtrudeGeometry does internally and transplant the extrusion from the z-axis to the y-axis. The logic is fairly trivial in the case of a rectangle with a straight extrusion path (like your examples here), becoming more complex in proportion to the complexity of the shape and the extrusion path, but it's still far more complex than biting a bullet and using the extrude-then-rotate method.

Allright I found a solution with rotation and translation, what I messed up was that I rotated the mesh,not the geomerty. But I'm still courious about the correct way of doing this. Working code:

export function createStorageLocation(storageLocation: StorageLocation) {
  const shape = new Shape();
  shape.moveTo(0, 0);
  shape.lineTo(0, 200 / 100);
  shape.lineTo(400 / 100, 200 / 100);
  shape.lineTo(400 / 100, 0);
  shape.lineTo(0, 0);

  const extrudeSettings: ExtrudeGeometryOptions = {
    steps: 2,
    depth: 10,
    bevelEnabled: false,
    bevelThickness: 1,
    bevelSize: 1,
    bevelOffset: 0,
    bevelSegments: 1,
  };

  const geometry = new ExtrudeGeometry(shape, extrudeSettings);
  geometry.rotateX(MathUtils.degToRad(-90));
  geometry.translate(0, 0, 200 / 100);

  const material = new MeshStandardMaterial({
    color: 'blue',
    opacity: 0.7,
    transparent: false,
  });

  const location = new Mesh(geometry, material);
  const axesHelper = new AxesHelper(5);
  location.add(axesHelper);
  location.position.set(
    storageLocation.startPoint.x / 100,
    storageLocation.startPoint.y / 100,
    storageLocation.startPoint.z / 100
  );

  location.updateMatrix();
  return location;
}

result: