As far as I know, Allow Override is already enabled for all apache sites.
Its specified in the file /home/user/conf/web/domain.com/apache.ssl.conf
And it sets it for the directory
/home/user/web/domain.com/public_html
All dirs below that will inherit that setting.
If you want to turn it OFF, you can do so in the .htaccess file in that dir or any one below that.