And you never integrated all commands, some are still bypassing TFM like /tree or /bigtree so we had to completely block them with TFM's or WorldGuarld's command blocker, or the damage is at least easy to undo.
And /tree is a world edit command if I recall.
/bigtree is an essentials command. It isn't logged by coreprotect and works in *all* worlds, even worlds where OPs cannot build. It was abused to bypass world permissions and that is why it got blocked. /tree is a worldedit brush-type command and is logged.