I can't read the programs, but it appears "mount-marks.ulp" is finding and using the defined origins of smd and other components.
Are you sure you want the origins as shown, rather than one calculated from the pads? I believe whoever makes the package can put the origin anywhere he wants it. It is not always in the same relationship to the pads as another origin might be.
For that reason, I suspect a location specified relative to the outline or pads would be more reliable from an electronic standpoint.
BTW, a rather small detail, a 3-pin smd transistor is not symmetrical in my view.
John