There's already a strong precedent for something like .well-known being disregarded — the ~/.config directory. It's the same idea, a special directory starting with a dot, and the objection seems to be similar, that it's awkward. In the case of the config directory it's that the storage for an app is spread between multiple directories like ~/.local/share and ~/.cache instead of one directory like ~/.vim
https://wiki.archlinux.org/title/XDG_Base_Directory
I support both well-known and XDG because I think the benefit outweighs that perhaps they could have been designed better. But I don't think that those who opt out of it could only be doing so out of ignorance.