Gah, regarding
Missing tracking for {'cert-nickname': 'Server-Cert', 'ca-name': 'IPA', 'cert-database': '/etc/httpd/alias', 'cert-postsave-command': '/usr/libexec/ipa/certmonger/restart_httpd'}
never mind. The cert is in the verbose output you sent! It is fine and issued by IPA.
So this looks like the tracking is simply missing. Can you run:
# ipa-getcert list
You should have two certs, one for Apache tracking /etc/httpd/alias and one for LDAP tracking /etc/dirsrv/slapd-REALM
If you have one for Apache can you provide the output of the list command?
If you don't then you can re-create it (this doesn't touch the certs themselves) via:
# ipa-getcert start-tracking -d /etc/httpd/alias -n Server-Cert -C /usr/libexec/ipa/certmonger/restart_httpd
rob