I had no idea it was asking me this second question. I completely forgot that it would. And the minibuffer where it asks it is the bottom left of my screen, while the dired buffer is in the top-right, this being a 27" Apple display at highest possible resolution, so there's no way I would have noticed it.
Is there a way to make this kind of question pop-up a new frame or some other more visual way of asking this?