Whoever decided it would be a good idea for ".well-known" to be a "hidden" directory is a complete fool. All it does is provide the opportunity for confusion, misconfiguration, skipped backups, missed git check-ins, forgotten updates and more. Literally the only people a folder like that is hidden from is the whoever is managing the web server.

Sure, if everyone knows what they're doing, it's not a problem. But we all know how long that assumption lasts.