I am one of many people who was confused by this change as well.
I agree that we should (at least) give a warning during startup. If you believe it's too easy to miss it, a y-or-n prompt notifying ~/.config/emacs creation would be much better, though I might be asking too much.
I don't think it will be an annoyance, because this warning/prompt should only occur in the first ever startup of Emacs, prior to creating any configuration file. If configuration exists either in ~/.emacs.d or ~/.config/emacs, the user should never see this message again.
Given the large number of people who seem to have run into the same issue, most of which are users who have years if not decades of Emacs experience shows that something should be done before the release of 27.
Having thought about it some more, I came up with this proposal: Emacs could check if both directories exist, and if so, provide an interactive choice for the user to pick which one to use. If the user don't want to have to answer this question every time Emacs starts up, they can delete one of the directories.
Regards,
Elias