I have added a FAQ entry to cover my understanding of the Touch Bar situation.
The API for the Touch Bar does not appear to allow non-front applications to affect the Touch Bar, except that Apple does this themselves in Xcode and Screen Capture and the like. So Apple knows and understands the need, but have not made the facility available for Third Party macro trigger style applications.
The Keyboard Maestro editor may support the Touch Bar in the future for use within the editor.
To use some sort of Touch Bar trigger will likely require an application to come to the front, steal focus out of the current application, and then allow you to trigger the macro and return to what you were doing. This is not ideal, but will likely happen at some point.
In the mean time, asking Apple to add Third Party APIs for the “Control Strip” section of the Touch Bar would be a good idea.