There is an appearance top level menu. All theme appearance settings can go below that menu.

When it comes to promotions etc I think it could be solved like this. WordPress should have a dedicated Donations & Promotion admin page with WP styling. Then all plugins using admin notifications for promotion or adds "billboards" could get rejected in the WP repo. If a row is registered it can be notified automatically by WP itself on activation.
Then users can configure how they want things to work themselves. Also everything is in one place. Order can be random, there can be default reminder etc.
It is a bit odd that the repo is used as a freemium promotion platform.