For default flags, the commands are nearly identical to the ones to set flags for the current world. Just add
/worlds and use the commands from set, control lists and unset.
/worlds defaults set pvp false - Disable PvP by default
/worlds defaults set command black - Allow executing commands except those which are added to the control list (blacklist mode) by default
/worlds defaults set command list add me - Add the
me command to default command control list
/worlds defaults unset fly - Don't allow or forbid flying as default like the plugin wasn't there