Comment 5 for bug 1788986

The sysv script checked for a Quagga.conf file, and if it's there, ignores the need for the other config files:
        # If the integrated config file is used the others are not checked.
        if [ -r "$C_PATH/Quagga.conf" ]; then
          return 0
        fi
...
          # check for config file
          if [ ! -r "$C_PATH/$1.conf" ]; then
            echo -n " (not started without config file)"
            return 1

Just touching the config files would not be enough as a workaround, as the systemd service files actually start the daemons pointing them at the respective config files:
ExecStart=/usr/sbin/bgpd -d -A 127.0.0.1 -f /etc/quagga/bgpd.conf

This will need some thought, or maybe revert to using the sysv initscript again.