The Karapoti has a longer top tube than the Punakaiki, however it can be run as drop bar build.  When your body is suffering from a gruelling day of riding you will need wider tyres for comfort.  Balloon tyre comfort made mountain bikes popular in the 1990's for this very reason.  The Karapoti geometry is designed for comfort, it can run dropbars with a shorter stem.  With a higher bottom bracket height than the Punakaiki, the Karapoti has better pedal clearance over rough terrain.
The main reason for choosing the Karapoti over the Punakaiki, is the larger tyre clearance, comfort and being able to move around the frame more. The Karapoti is also available as a Pinion Gearbox Frame.