If one of the CA certificates used during CA-less install conflicts with a system-wide CA certificate, the install succeeds, but is broken:

• As /etc/httpd/alias uses the system-wide CA certificate store by default, it will contain both of the certificates, which might lead to httpd using the "wrong" certificate.
• The system-wide CA certificate somehow finds its way into cn=certificates,cn=ipa,cn=etc, so a subsequent replica install or ipa-certupdate puts it into all the places in the filesystem where IPA puts CA certificates, which broadens the issue to all IPA services.

This issue was observed by Peter Pakos on freeipa-users: https://www.redhat.com/archives/freeipa-users/2016-July/msg00360.html.

Make sure this setup works.