Unless of course he listed Manakau as his home town although his parents married and he was born in Timaru in the same way that everything else is mixed up on that listing maybe the census chap asked the wrong question?
The heading on the column in question is 'Birthplace' and part (2) would have been relevant - 'If born in any other part of the British Empire, write the name of the dependency, Colony, etc., and of the Province of State'. This would have been filled in by the head of the household - not by the census enumerator, who simply distributed the forms and then collected them after census day.
However quite often it seems that people entered where they
thought they'd been born rather than the true place - if he'd lived in Manukau as a child he might have though he'd been born there although actually born elsewhere.