Very good point!
The pad will be generated at the center of the symbol as given by its bounding box. This is in most cases OK, but, as you point out, will not work for asymmetrical shapes where the desired center is obvious to a human looking at the drawing, but not to the software. Will update the document to reflect this.
There is a way to deal with these shapes also, but it involves manually positioning the crosshair at the desired center before doing the conversion. We have now added this to the tutorial document also.