Yeah been wondering that as well. The documentation doesn’t really provide any useful information here. @eve
I’ve seen people on the forum claiming that it does nothing, that it makes pages unavailable to desktop browsers and a few things in between. But since Bubble doesn’t have any native app support, I’m leaning towards it doing nothing apart from what it says on the tin, showing a pop up 
This page is a native app
Check this box to build a native app and if you want this page to be the app submitted to the app stores. Clicking this checkbox displays a popup listing tips for building a native app.
Note: This feature is in beta.
Edit: Not sure why a pop up is in beta, that’s why I’ve been wondering.