phpBB 3 sensibly strips  any PHP tags in templates ;
But as they are in the same format as the short tags allowed by PHP, this also removes any XML processing instructions used in RSS, Atom file generation, etc. ;
Whilst you could adapt the phpBB code to check for short tags being set on, you would also need to put such checks in the code where you were using templates with the XML processing instructions.
There are a few solutions, the first being to prepend the processing instruction to the returned code from the “assign_display”  function ;
The second and ordinarily preferable method is to adapt your template(s) and assign the processing instruction using either the “assign_var”  or “assign_vars”  functions to a template variable ;
Either of these solutions also allows for the processing instruction to be dynamically tailored to suit encoding changes, etc.
 function remove_php_tags in <PHPBB_ROOT_PATH>/includes/functions_template.php.
 In <PHPBB_ROOT_PATH>/includes/template.php.