First off, let me introduce myself. I've been doing bracketology and RPI/SOS/etc. calculations for various D2 sports for several years. Since D2 sports are moving to NPI this fall, I took some time a few months ago to learn how it works and how to calculate it. I'm here because I saw there was controversy surrounding the D3 hockey NPI. So I'm not a D3 hockey fan, just someone who's interested in the NPI.
A few things that I think need to be clarified:
The 25/75 weighting of winning percentage and SOS is misleading, as there is no time when a team's overall winning percentage and SOS are combined in that way. The NPI doesn't even output an SOS figure; that's created after-the-fact by averaging the opponent NPI ratings (not something that ever happens within the NPI calculation).
Rather, the 25/75 W%/SOS is applied to each individual opponent, in which the SOS part is that opponent's NPI and the W% is 100 for win or 0 for a loss. This is where the quality win bonus is added in, if applicable (and it also applies to the half-win from a tie and the 1/3-win from an overtime loss in the regular season).
If you've got 9+ wins (adjusting for overtime and ties as well as home/away weighting) and the total for a win is less than your NPI, that win is discarded as long as that doesn't bring you below 9. This applies also to the win "parts" of ties and overtime games... but the loss parts are unaffected. (USCHO's weighted winning percentages, from what I can tell, account for home/away weighting and overtime, but not for excluded results.)