A good question.
A local answer.

Choose one longer ferry or rail outing that fits the timetable and leaves time at the destination.

A guided tour adds architectural and backstage context when that is a particular interest; check what the current tour includes.

If wind or rain makes the exposed walk unpleasant, switch to a shorter harbour outing and save the coast for a clearer day.

Choose the base from the actual arrival and onward flight times, not just the number of nights.

Allow enough time for the long return trip and choose a beach with changing facilities that fit the plan.

Choose the beach by current swimming conditions and supervision, not only the shortest public transport route.

Compare the airline's minimum check-in time with a realistic arrival delay and immigration buffer, not only scheduled flight times.

Save the daughter's preferred outing for their shared days and check weather before fixing a beach or regional trip.

If the margin is small, move the flight later or stay overnight rather than assuming an early ship arrival guarantees a quick exit.

Check current Vivid dates, installations and traffic restrictions before assuming a waterfront room is the easiest base.

Check the current Transport for NSW journey planner for the exact train and accepted payment before leaving Central.

Treat the zoo as the main timed visit and decide which one of the other two areas deserves a relaxed afternoon.