Perhaps I am the only one, but I am not sure if I like the idea of a Magic Toolbar that changes based upon the app you are in. One of the things that I like about the function keys is that they are very system focused and will work no matter where you are. If developers are allowed to make the touch bar all about themselves and their app, what happens if you want to alter the screen/keyboard brightness and volume? What if you want control over play/pause and your music tracks despite the fact that you might not be in that app? I certainly would not want media specific functions only available in Spotify or iTunes, for example, because that makes them far less useful.
I suppose that Apple could require that all of these functions still be accessible at all times, but that would really cut down on the amount of space developers have to work with and would make it less useful. And if they don't mandate that these system functions are available at all times, then developers can easily make our machines less useful, too, if they get rid of these functions within their apps.
Additionally, what would developers use this space for? It seems to me as if it would end being nothing but a place for functions that can already be done extremely efficiently with existing keyboard combinations. In Safari, I wouldn't need a reload icon in the touch bar, because Command + R already works and is just as easy (or I can just use the trackpad).
Personally, I can see Apple locking down access to the touch bar, and in this instance, I think I almost might prefer that because this seems like it could be a messy gimmick otherwise. If they do let developers have access, I hope that Apple gives us an option in SysPref to override their modifications and give us access to the standard functions only. But, it is Apple, and this isn't something they like to do.