In most cases, the score for DNF is the same as the number entered plus 1. It would be different in a series longer than a regatta.

I have seen race insurrections in past where DNS is entries +2 and DNF is Starters +1.  I think the point about what the program is actually calculating is very important.  

I personally lost a Sone Cup after scoring 3 First place finishes and then retiring (blowing 35Kts) from the last race where there were only 2 boats on the water for the last day.  I expected to get a 4 and my 7 points would win on a tie breaker against 2,2,2,1.  I was very surprised when I was scored a 9. for the last race.  I didn't mind getting the number of entries +2 but this was back in the days when the Saturday of Stone Cup was an HDA counter and boats had to pay extra for the Sunday and complete the regatta.  Only 2 of us entered the Sunday but the program couldn't deal with a different number of entrants for the different days and still score it as a single regatta.

Not trying to plug one program over another, but the ability to assign different values to scoring codes is just one of the many reasons I like SailWave. I have yet to run into a situation I can't handle with it and I just need to know one program. That said, it can be quirky and is not easy for some people to learn

My understanding is that the change in 44.3(c) is intentional.

It is probably the case that many of the scoring programs haven't caught up with this change, or have previously had bugs. Over the years there have been numerous bugs in scoring software. When serving as PRO, I have often corrected a score which the software got wrong. This is particularly problematic when the SIs alter the scores for DNF, DNC, etc....  I'd strongly recommend checking one's own results and filing a scoring inquiry if something looks wrong.