If one could create php code in ATutor content, they could do serious damage to your system with relative ease.
This can not be modified with an admin setting. Admin setting only allow instructors to upload php files if the php extension is removed from the illegal extensions list.
I use php myself in the course I teach, but only in files I've uploaded with the file manager after disabing the php illegal extension. You probably don't want instructors uploading php scripts without you knowing about it.
See the activities in the Learning to Learn course, linked from the ATutor demos, for examples of php scripts running with a course.