In the earliest days of Final Fantasy XI, you couldn’t alt-tab without crashing the game. Thus, the Windower program, a little add-on designed to force the game to allow alt-tabbing like basically anything else in the world. The add-on was also disallowed, but the developers eventually adopted a “don’t be an idiot” approach to it; you have native window support now, but if you still want to use it for its other functionality, just don’t shout about it in-game and you’ll probably be fine.
Of course, it’s hardly the only unofficial modification that affects a game’s functionality; multiboxing in World of Warcraft, various map add-ons for City of Heroes, the DPS trackers for Final Fantasy XIV. Every game has stuff that’s not technically allowed, but isn’t any sort of cheating tool; it’s just there to improve your life as a player. So have you ever run unauthorized MMO modifications? Not cheating tools, those are a different story, just mods that alter the functionality of your chosen games?