Package Modification for Hook
The actual telling of cPanel&WHM to change the limits would be handled via the APIs hooks intercept those requests. I'm having a difficult time thinking of a scenario off the top of my head so let's make up an absurd scenario - what if you had a new tech that wanted to change the amount of CPU accounts on a specific package could consume to 0.001% of the CPU this hook could intercept that and block it because it's a ridiculously low limit to set. It's a bit of an absurd scenario but I hope it conveys that APIs trigger changes hooks can intercept those changes (e.g. useful for communicating with billing systems) and even deny those changes.