I have many websites which use PHP short tags on my server and was wondering if I can enable this globally some place? I entered it directly in /etc/php/7.2/apache2/pphp.ini last night and thought it had done the trick, but then when I removed the directive in a Site in ISPConfig, it seems it's is not using the one in the php.ini I altered. Thanks.
You just edit the global php.ini file, but that's not /etc/php/7.2/apache2/php.ini. You must either edit the cgi ini file, if you use fastcgi mode, or the php-fpm ini file, if you use php-fpm mode. The apache2 php.ini file is just for mod_php, which is not used anymore today.