Interesting case. Well, how I'd look at this.
>ID overrides the server rules.
>You're not allowed to pirate ships within Kusari space.
>You're allowed to attack Junkers and Gallic Junkers anywhere.
Therefore, if said Junker is in transport ship, and ID override the rules, ID is specifically prohibiting you from issuing a demand in accordance to Rule 3.3, while specifically stating that you're allowed to attack them.
With ID's overriding server rules, this only means that in you're not allowed to make acts of piracy against junker transports in Kusari, but you're allowed to kill them on sight.