Consider Sendmail as a cautionary tale. One more than one occasion I have seen a busy sysadmin manually edit a .cf file and forget to backport the edit to the .mc file. The next time someone regenerates the .cf from the .mc you have a vanishing edit.

Yes, the sysadmin was clearly at fault. No, this is not a deal breaker, as seen by the longevity of Sendmail. But a config file that gets pushed through a preprocessor has a more complicated life cycle than a "static" equivalent.

If your organization has comprehensively embraced ansible/chef/puppet/etc this may be a non-issue, because all of your configs might be generated. Just food for thought.