Global Apache Alias, ignoring virtual hosts

You can try to add this before all your virtual host :

Alias /.well-known/acme-challenge/ /var/www/letsencrypt/.well-known/acme-challenge/

#Bypass Auth
<Directory /var/www/letsencrypt/.well-known/acme-challenge/>
Satisfy any
</Directory>

#Redirect before other rewrite rules
RewriteCond %{REQUEST_URI} /\.well\-known/acme\-challenge/
RewriteRule (.*) /.well-known/acme-challenge/$1 [L,QSA]

I came across your question with the same letsencrypt acme apache alias problem. After reading through the apache documentation, I still don't undestand why the global alias doesn't work as expected (according to the documentation it should).

Anyway, here is a workaround that uses RedirectMatch (which according to the documentation is evaluated before alias). It requires one additional host and one global configuration file:

1. Create an additional (sub)domain / host that only serves acme requests, lets say "acme.mydomain.tld"

2. Create (and enable) a global configuration that redirects all acme-requests to that host, excluding the host itself from redirection:

   <If "%{HTTP_HOST} != 'acme.mydomain.tld'">
       RedirectMatch "^/.well-known/(.*)$" "http://acme.mydomain.tld/.well-known/$1" 
   </If>
   

This works for all my VirtualHosts which had problems with the old alias approach.

According to Apache 2.4 documentation you have these options:

There are two basic types of containers. Most containers are evaluated for each request. The enclosed directives are applied only for those requests that match the containers. The <IfDefine>, <IfModule>, and <IfVersion> containers, on the other hand, are evaluated only at server startup and restart. If their conditions are true at startup, then the enclosed directives will apply to all requests. If the conditions are not true, the enclosed directives will be ignored.

May be you can give it a try use one of the containers mentioned above and add the alias that you need to be globally for all requests. See details here: https://httpd.apache.org/docs/2.4/sections.html#mergin.