Yep, I'm absolutely sure it's only to replicate the touch-screen functionnality when docked.
It doesn't matter if you can't press any button while holding the right Joy-Con upside down, because if you use the touch-screen, you can't press any button with your right hand while touching the screen anyways. So basically, when you hold the Joy-Con upside down to use the pointer, the buttons will most likely be deactivated. If some games need you to use the right Joy-Con joystick while using the pointer, that would bring a new problem: the touch-screen itself, as you cannot use that joystick (or any other button) while touching the screen. The purpose is quite simple: to give you the SAME controls and/or gameplay as if it is docked or not. That's a very important thing to remember. You should be able to do the exact same things docked or on the go.
So yeah, I'm confident this will be useful in games like Super Mario Maker where you gotta pick and drag items on the screen or to navigate through the OS... But for FPS or games like Pikmin where it needs more than just a pointer? Forget about it or you'll be disapointed.