Well essentially I want to know why the script scanning isn't running on a script file being executed, regardless of where it is located. If it was then theoretically there would be no requirement for a rule.
The merging of several shields (script/network/P2P, etc.) into the remaining shields shouldn't lessen the protection.
Your example of the actions is flawed as there would be many instances of legit .VBS software that has to run wscript.exe. Any blocking and quarantining should only be done if it is found to be malicious.
Another point being those who have the Hardened Mode set to Aggressive may have bypassed the deep screening function.