Since all of the molds that MM cuts are lathe bored and his process necessitates a minimum 0.18" flat meplat you will not be able to produce a true complete RN boolit mold with his software. You can, however, shrink the meplat down to the minimum size and use the correct nose profile selection to make a RNFT boolit mold. Which in many cases is a better choice then a RN boolit anyway. Let’s not forget that Winchester FMJ pistol rounds are available in a RNFT design and Winchester advertises them as having superior accuracy compared to conventional FMJ RN bullets. In addition the presence of a flat meplat considerably simplifies nose punch selection for sizing since one can then use just a simple flat nose punch which contacts the boolits meplat. I use just a simple short length of piano wire the right diameter to chuck into my Lyman sizer cut off nice and flat.
40-cal is not a caliber I personally like, but I threw together this example boolit in MM's design program in about a minute flat doing it the same way I would do a boolit for 45-ACP which if I'm not mistaken should be similar to what you want to do only on just a slightly larger scale.