My understanding is that much of the ground under the tanks was full of toxic waste and so that had to be remediated at a high cost. That cost was most definitely included.
The works done by the council were not what ETNZ, or the marine community wanted. The plan from ETNZ would have cost slightly more but resulted in 50 % more retained infrastructure in the form of Super yacht facilities, of which Auckland is very short. Instead the council sought to load up cost for which they were liable onto the America's Cup bill, despite a lesser return. There was also a threat of legal action again