An incoming call isn't an alert. It's a highly time sensitive notification.
An alert is something that blocks further input until it is dismissed. Something along the lines of "Are you sure you want to disable encryption?" or "This item can not be deleted because it is locked."
I think that it was providing shortcuts for interacting with an alert already displayed on the main screen. Apple's worry, I'm assuming, is that alerts will be displayed only on the bar and people without the new Pro will not notice them.
Do as I say, not as I do?
It's interesting, then, that they explicitly showed the Touch Bar being used for alerts in the design video (when the user received a FaceTime call).