I would say no as it was a penalty imposed in a hearing.    

Erik,
First to make sure that we are on the same rules version, I am reading the 2021-2014 version since you are going to be using your program in a matter of 2 months.
Rule 86.1 tell us what can and cannot be changed. 86.1(b) lists rules that cannot be changed by the SI's. Included in the list are rules in 86.1(a). 90.3 Scoring is in Part 7, which is one that cannot be changed by SI.
That could make your scoring program simpler.
Kim

Rule 9.3 is in part 7; 86.1 says rules in part 7 can't be changed. So 90.3b requires DNE to always be included if the scoring system provides for excluding one or more races. I assume someone can make an argument that since you can define your own scoring system you can define a system that doesn't include DNE, but I think that would violate 90.3b and would be an invalid modification of the rules. 

Thank you all for the help! This definitely make the program a little easier to write.

NOR/SI can change the whole of Appendix A if they are foolish enough.

What they can't do is change the following rules that result in DNE:  rule 2 and rule 69 (rule 86.1(a)).

The only remaining rule that makes a score non-excludable is rule 30.4 (BFD):  this rule is changeable if you wish, but given the presence of U Flag and other starting penalties, why would you bother.

Have a play with Sailwave from https://www.sailwave.com it is totally free and you can see how it allows scoring codes to be configured, including the addition of user specified codes - so as new codes come into play user can add or modify the codes as necessary.