If I create the same directory structure but without "initial dot" I can see the content of prova.txt: https://www.cosmogonia.org/well-known/acme-challenge/prova.txt
Then, I've seen that all my "http" Virtualhost had set the DocumentRoot, and now I've delete it as suggested here: RedirectSSL - HTTPD - Apache Software Foundation
At last, I do not know if this can answer your question, but looking into my DocumentRoot directives I've seen that it is not always the same, but I don't know if this could be a problem for the obtaining of certificates:
Here my DocumentRoot https for the FQDN:
/var/www/html
Here my DocumentRoot https for a standard website (`/var/www/website-domain/public_html/):
/var/www/cosmogonia.org/public_html/
Here my Letsencrypt Virtualhost:
Alias /.well-known/acme-challenge/ /var/www/letsencrypt/.well-known/acme-challenge/
<Directory "/var/www/letsencrypt/.well-known/acme-challenge/">
Options None
AllowOverride None
ForceType text/plain
# avoid access to anything not resembling a challenge
RedirectMatch 404 "^(?!/\.well-known/acme-challenge/[\w]{43}$)"
</Directory>
.. I hoping to understand your observations
Thanks!