No warning just pops up, usually they have to redirect the user to manually open settings, or at least open settings for them. It's not a simple dialog, they have to remember instructions and then apply them within the separate settings application.
And then no auto updates on top of that.
The user has to enable a setting buried deep in the menus -- easy for someone tech savvy, but not for the typical user. They need to do that before they can even install the alternative app store, since you cannot distribute an
alternative app store via the play store. Even once you've done all that, every app install through the alt app store must be confirmed by the user through an interstitial dialog, which also means the alt app store cannot auto-update apps. It all makes for an awful experience that even those who know how to do it don't want to deal with.