> input X and then wait for Y before doing anything when there is only one intention the user could actually have in mind

That's obviously false, the second possible intention is... cancellation. For example, you can bind Q,Q to quit the app (and no other key is prefixed with a Q), but then you could press Q mistakenly or change your mind at the last moment.

But you continue to argue with your own strawman - nothing about helpful popups changes the underlying behavior. So if your magic design is to run XY just on X press, that would be bad design, but you can still do it! And the popup will never appear because the action is complete, so no help needed.