(Debian 9 and Virtualmin GPL v6)
Although the Apache mod_php is disabled and not a option (the parent server-vhost uses php-fcgi), any new server alias in
Server Configuration>PHP Versions displays
This virtual server is using the mod_php execution mode for PHP, such does not allow per-directory version selection.
Everything works, its not a big problem until you run something like
virtualmin modify-web --all-domains --php-version x.x.x.
The process stops and exits when it tries to alter a domain alias.
Where does Virtualmin gets the info that a domain alias is using only mod_php?
Note, that after disabling mod_php I had to remove
php_admin_value engine Off from all the vhost conf files (in case this is the variable Virtualmin is looking at).