Is there a way I could make rules apply ONLY when a toolcupboard is set? 

For example, I want to prevent unfriendly damage to a structure only when a toolcupboard is protecting the area

have you tried AuthorizedDamage combined with CupboardOwnership flags?

• AuthorizedDamage - Allows players to damage entities they own or have cupboard authorization over

• CupboardOwnership - When enabled with AuthorizedDamage will treat entities outside of cupboard range as unowned, and entities inside cupboard range will require authorization.