There are some servers where I have change the Alert Configuration from the default template, I.E. unticking the "CLR Enabled" so that it no-longer alerts for this condition. Is there a way to find all servers that have had these changes made?
Not currently, at least not without customization to build your own alert template reports.
Alert template reports are planned for a future release to help manage application of templates and audit status of what instances have modified templates.