I appreciate this warning banner, and I'd appreciate it even more if it included a clear button right there by refresh. A lot of the time (maybe even most), I don't want to run my tools on a selection. I've added a clear button to my quick access, you can find it on the ribbon somewhere (map view only), and newer versions have a button in the bottom corner, but that only shows up in map view. If you're in a layout, your window's in the way, etc, you're out of luck. Even if you did have the button always visible like I do, a quick button right there would be super useful in many circumstances. Redundancy is not always bad.
Another solution might be to just have a switch to flip off running on the selection - retaining the selection, in case you were doing something else with it.