Hi @btbogan,
The reason that you need to change the Favicon is that we removed that feature all together in our theme because the WordPress already has that functionality now and it is redundant to maintain a feature which is native now.
That is a one time upload and not related to any other settings. The other case you mentioned about the toolbar is not reported to us and it is a very strange issue. Please consider that our theme does not have anything to do with the feature you said which is available from Users > Profile. That is a WordPress native feature and not related to our theme. Having said that, our theme does have an option regarding the Toolbar when it comes to showing it in the Cornerstone or not. That specific item is changed also and now it is in X > Theme Options > Settings Icon in the left lower Corner > Preferences> WordPress Toolbar:

The reasoning behind that specific case is to provide a way that you can set stuff while being in the builder and not have to go back to WordPress Dashboard.
Regarding the app icons, it is not available anymore and you will need to use the HTML meta tags added to a Child Theme to have that option.
Thank you.