This is answered in the man page:
enforce_for_root
The module will return error on failed check even if the user changing the password is root. This option is off by default which means that just the message about the failed check is printed but root can change the password anyway.
Simply add enforce_for_root
to a line by it self in /etc/security/pwquality.conf
.
Note that root can bypass this more or less at will by injecting their password hash. There's ultimately few things that stops root from ignoring configuration on Linux.