“You could be missing 3 points of knowledge” means points from the maximum. Could this apply to CF as well? Not just prerequisites? That part of the quote doesn’t mean 3 points from 50 on your prerequisite. You’re not that close to 100.
“but create 5 points of new knowledge,” this can happen when you’re close to the max. I think since 100 points represents current knowledge that applies to both CF and prerequisites. If you learn new knowledge, it adds up the points for whichever skill youre trying to build.
It seems that knowledge is a quantitative thing that you add. You add it for the points system.