If this means that ~/.emacs.d/ didn't exist when Emacs was first
started, then I think it's OK for Emacs to default to ~/.config/emacs,
because neither of the two possible candidates exist.
So now I don't think I understand the confusion.
The confusion is that once I start Emacs without any configuration, the $HOME/.config/emacs will be created, and after that the $HOME/.emacs.d will never be used, even though I don't actually have a configuration yet. All I did was to start Emacs once.
I don't think the $HOME/.config/emacs should be created until there is actually a configuration to save. Or, alternatively, before the user have confirmed where they want the configuration directory to be created.
Imagine a user starting Emacs once, and then immediately closing it without touching a single option in the application (this will create the $HOME/.config/emacs). They then go to a Youtube video or blog post to learn about how to configure the application. They create a $HOME/.emacs.d/init.el and then ends up not understanding why the config file is never read, even though they followed the instructions exactly.
Since the $HOME/.config behaviour is new, it will not be easy for them to figure out why nothing works and they will give up, perhaps never trying Emacs again.
That is my concern.