I noticed that cert_dir always gets certs joined onto it. However, /etc/pki/ca-trust/extracted is a dynamically created directory generated by the update-ca-trust script and the pem subdirectory is just one of the many created by this script that stores PEM bundles. None of them have a certs subdirectory AFAIA.
I think the probe will find the legacy /etc/pki/tls/certs right after and sets cert_dir to that.
Can this directory and possibly others like it be separated from the directories that do have a certs subdirectory?