This is, funnily enough, one area where Square is not unique. Using the logitech gaming software - or the equivalent from any other manufacturer of keyboards and mice - is a violation of pretty much any online game's TOS. Blizzard, Riot, Valve, etc could all issue a permanent suspension for the use of that software, and Blizzard's a bit infamous for actually having done so.
Of course, since it's packages with the hardware, you don't get a ban just for having it. What they don't want you doing typically is "Pushing 1 key sends 5 key presses" or "This macro auto repeats while I'm AFK" and so on. And even then, enforcement is typically low to nonexistent if it isn't super blatant. But on the books, it's typically against the rules.
Also, from SE's website:
Sadly, this tends to be a bit more reasonable than the Lodestone posts and live letters, which typically suggest a stricter stance than what's on SE's support website. But one could interpret this to mean it is ok as long as 1. It doesn't allow unattended play and 2. It does not interact with the game.■Behavior that disrupts the game balance
Square Enix strictly prohibits the use of third-party programs or tools as these disrupt the balance of the game. Third-party programs and tools that permit automated or "absentee" play are prohibited. A Game Master (GM) may speak to players to investigate and confirm "absentee" play, and if the player continues with this behavior, contrary to the GM's instructions, they will be treated as participating in "absentee" play and subject to penalties.
Accordingly, the following activities are prohibited:
- Modifying, analyzing, integrating, and/or reverse-engineering game software or data.
- Creating, distributing, using, or promoting utilities that interact with the game.