This bootstrap is invisible to the user, you don't need to touch the java to use kivy. That said, kivy has some cool sister projects for using the normal java api - pyjnius for accessing java classes directly from python, and more recently plyer to provide a more pythonic wrapper to common things like vibration, sensors etc.
(The above is also mostly the same for the ios build process).
> Is it better than PhoneGap etc and closer to native apps?
I would say more that it is just different, with advantages and disadvantages of its own. It doesn't use native widgets (though it's possible to create and use them in some ways with pyjnius), so it isn't different in this sense.