will these tweaks stop scripts, or only exe files?
From what I understand, Application control only applies to exe files.
If you want to block scripts, you will also have to make block rules individually for each script interpreter.
It depends on the situation: is the executable running the script being restricted or not? If yes, then it'll apply to it too.
The script cannot just do things without using the Windows API, not possible. The script is interpreted and the contents of the script is used to determine the code for the execution of the actions, which then bonds down to using the Windows API -> NTAPI -> triggers any hooks from Kaspersky, kernel-mode callback notifications, and the such.
I believe Kaspersky work with MSR hooks with the hyper-visor on a system-wide level (virtualization but it allows them to bypass PatchGuard problems on x64 systems); they probably use user-mode hooking also with injection to the restricted programs, and device drivers for kernel-mode callbacks.
Enjoy the internals info, it should be right.