What is the effect of the choice to "set up as new iPad"?
CONFIRMED BY MYSELF on my new iPad mini 4 and iTunes 12.

If you select "Set up as new iPad" and hit Enter you'll get a new window with "Sync with iTunes" message and a blue button with white letters Get Started.
After hitting this button you'll get a iTunes window for your attached device with all the relevant information, Backups and other Options.

In other words, if you select "Set up as new iPad" * NOTHING IS CHANGED IN THE ATTACHED DEVICE * it is only attached to iTunes for subsequent actions.