VHFRT, at the time that EBA was done the government had legislated (or about to can't remember the exact timing) increases in the super guarantee.
For salaries that were non inclusive of super that became a cost to the employer.
For salaries that included super the employee effectively paid for it as they had signed up to a deal that was super inclusive, so the percentage amount of the super could vary without impacting the overall cost of the deal, in short. Any increase in the super guarantee above 9% of your gross pay was funded by reducing your take home pay.