actually what you have there is a weird pyramid, not a cone. I don't know how you look at it but there are 9 points, one of them being in a different plan than the others [1 3 1] therefore you cannot get a flat rectangle. The [1 3 1] point is the top of the pyramid.
if you are not sure about it draw a cartesian coordinate system on a paper and then add 9 dots, each coresponding to the coordinate points that you have ([0 0 0], [1 0 0],...)
now connect the dots as the coordIndex specifies. You will get some kind of a pyramid, with some unconnected points in the base.