These are just guidelines. You can submit apps to the App Store that violate them if it makes sense for your app; people do it on iOS all the time.

They're not going to control it for any apps, App Store or non. It's a guideline. They're just saying, "Based on our research developing this thing, these are the things you do and do not want to do when developing for it." Same as any other company that makes any other thing does.

Only the currently selected foreground application gets to use the TouchBar and display content on it.

Which means apps distributed outside of the app store when they have focus are allowed to put whatever they want on the TouchBar and you are allowed to close and delete the app.

Problem solved.

I'm pretty sure its only talking about App Store apps.

But maybe they'll make it hard or even impossible for apps outside the MAS to use the touch bar.