I honestly don't see the phone app as that big of a deal. Granted I would prefer some kind of OS integration but think of it this way:
I'm sat at my PC right now and my phone is literally 30cm from my right hand and when on the couch, my phone is always next to me. To spend a few seconds to pick it up and use and app in my opinion will be quicker than navigating through menus on screen.
Remember that when docked, we have no touch screen on the switch, so all match making, invitations each will need you to scroll using the pad. I quite like the idea that instead of that, using a couple of touches on my phone to achieve the same thing.
However this all boils down to the UI of both a matchmaking system in game vs the app design, which could be horrid.
Preferably, we should have been given a choice (i.e both).