But JSON doesn't support comments which are pretty nice in a config file. You can do the ugly comment as property stuff, or strip them out, but you're getting away from the One True Format.
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.
Er, only if the application doesn't run the preprocessor itself.