If you force me to migrate, I'm probably ditching your software. The inability to keep a stable user contract is a deep flaw that impacts too much software these days.
Everyone should do what emacs does (and a lot of software does): first look for .emacs for a config … not there? Check .emacs.d … still not there? .config/emacs …
That's not exactly what emacs does: if ~/.config/emacs isn't there, then it will default to creating ~/.emacs.d/ and ~/.emacs, even if the XDG env vars are set. Basically, emacs supports XDG config if you really want it to, but it's not the default way of using emacs. And of course, it only uses ~/.config/emacs, none of the other XDG folders. If you download a package from MELPA, that's still going to .config/emacs, as far as I know.
But also not without the downsides, because what do you do if multiple files are found? And how will you communicate that to the user, if at all? Lots of room for confusion here: "why aren't my changed taking effect?!", "where is this setting coming from, it's not in my file?!" and things like that.
Things like bashrc and vimrc have been "standard" for decades; that's not a "non-standard configuration", it's what everyone uses today. And Neovim only supports ~/.config/nvim/init.vim judging from the manpage(?) If it doesn't then this only underscores my point that all of this is apt to lead to confusion.
Either way, it had a clean break from Vim and didn't have to deal with people who have been using Neovim for decades (lots of things are different compared to Vim and it's not intended to be compatible in the first place).
Respect the user.