This has been discussed a lot here. You can find some of the earlier threads by searching
The summary is that this is an Internet standard from RFC 5785 and also adopted as an industry standard from the CA/Browser Forum. Let’s Encrypt is not allowed to change it. Part of the purpose of this standard is to make it easy for hosts and sites to block users from posting files that will have a special meaning. For example, sites that operate a forum or let users create their own pages don’t want to accidentally allow users to post files or pages that will affect how browsers or search engines or certificate authorities treat the entire site. Therefore,
/.well-known is standardized as a place where things that do have a special sitewide meaning or site-effect can be placed.
It’s always annoying when hosts prevent customers from obtaining certificates or using HTTPS, but the remedy we have available for that is to widely publicize what particular hosts do and don’t allow. For example, we have quite a popular thread about this: