the "na" variable is for number of add ons, and the "nr" is for number of rebuys. If you look to penalize one point for either, it's as simple as adding this to your formula: "- na". If, for example, you want to penalize 3 points, it would be this: "- 3 * na"
However, to my knowledge, the program cannot directly correlate round of rebuy into the formula; however, in the game notes, you can see when the people rebought or added on, and adjust the points manually that way. My suggestion for doing what you suggest is this: Make your formula be n - r + 1 - nr. Track on paper or excel who rebuys and what round, etc., and adjust the points as you are able to. You are able to adjust during the game. By this method, only the 2nd level would not require any adjustments.
That's the best way that I'm personally aware of, but perhaps someone else may have a different/better way to do this...