I'm not familiar with Centos, so cannot tell what's wrong with your setup.
Reading the documentation here
, I saw that it uses the key/cert files in both the main and the vhost part of the configuration. I guess this is done because it somehow it defines a default ssl vhost.
Are you sure you don't have a _default_server (or wildcard server "*:443) that needs the certificates be in /etc/pki/tls/certs.
Without the output of "apachectl -S", we cannot be sure if that's the case. You can check the *.conf files for something like: "<Virtualhost _default_:443>" or "<VirtualHost *.443>