People have been using uTorrent to patch since Alpha. I highly doubt S-E cares. When they say third-party program, they mean things like windower and bots, things that give people an unfair advantage. Not patching through torrents. If it was against the ToU, you wouldn't see fansites like ZAM and FFXIVCore that had threads on how to patch by using torrents. A lot of stuff got removed at S-E's request, but that was never one of them.