from my understanding in vic- could be interpreted wrong, any non stnadard engine needs engeineering unless it was offered as an option in the same chasis from the manufacturer released in australia.

also any modifications increasing torque or power more than 10% from standard needs engenieering. as well as any change to emissions etc.

so from my understanding, yes you would need to engenieer it twice- technically, but if your stock motor had the new turbo, air filter and intercooler fitted, but was tuned for low power/economy, they would already be engineered as well as your engine number, possibly then not necessitating the 2nd engenieering.