Both of my PCMs still have the misfire stuff activated, I wanted that to stay in there since i'm still on my stock cam on both vehicles, why delete something when I don't need it gone? And i've tripped P0300 on accedent a time or two myself (not having a plug wire on or something) so it works.
In my experiance, even when I still had a stock PCM, and i felt a misfire, i never set anything off...