The software you are referring to (scoring points for targets and VUK hits) is not software written into it to specifically address the mode or situation. Those points for targets and VUK hits are the same regardless of situation, and the game does nothing “special” (as it does for AFM and Jackbot).
The rule you cited even goes on to definitively, specifically, refer to Spider-Man:
“On Spider-Man however, since there is no game rule written for that situation, this would be considered a stuck ball and the player should attempt to trap the other ball(s) in play and request assistance.”
Your last statement about opinion says that you know all this, yet chose to override the rule. This is fine, since NYCPC is not a Circuit event, but if you are going to override some of the IFPA/PAPA rules for an event, exceptions need to be noted in advance, rather than discussed after the fact.