I was looking at other software packages and found a nice option for the skins game. To make a natural birdie (gross score birdie) beat a net birdie, the option is to decrement the handicaps by .5. So a gross birdie on a par 4 would be a 3. The net birdie for another player would be a 3.5, so the natural birdie wins. This would be a nice feature to implement in a future update.