Would this be fixed by just setting these configuration files to be "configuration files"? (this is my silver bullet)

If we don't need to change core apache settings like we recently changed keepalive, yes.  If we make changes, users/customers would have to migrate to the new config files on each appliance and possibly cause things to be DOA on upgrade.  I'd rather better understand what customers and users would be modifying in the configs and provide a way to externalize these changes in a separate config file that is loaded last.

Closing.  We need to ship our configuration with the rpm as regular files so we can upgrade a complex of appliances without having to visit 10s of appliance to manually diff/apply configuration changes with each version upgrade.

Users could try the solution of storing their changes to the apache configuration in a uniquely named conf file that loads last such as /etc/httpd/conf.d/z_user.conf.  In this way, only this single file would need to be tested with each version upgrade to ensure newer cfme and apache versions still use the same syntax for the changes that the user wanted.