Using SCA checklist for eg apache in different installation folders

I’m wondering how to use eg CIS checklist for apache in case of having more than a fistful of servers having apache installed in different folders, eg:
/etc/httpd which is the default
/opt/application
/opt/httpd
and so on. I know that I can export all fixlets and analyses into one file and edit the relevance using “search and replace” but this seems to be a strange way in my opinion.