yeah. this is all true. my response was mostly for actually cracking the software used to perform botting. Sqaure Enix themselves are not allowed to directly acquire or even reverse engineer any of this. that is, assuming the domain/software/website owner(s) has such terms in effect. if so, accessing those services would tip the bias in favor of whoever runs those sites. in this case it would be Square Enix playing the defendant... however unlikely that might actually may be. LOL! but keep in mind... if it could somehow be proven SE violated any of those terms, then it would easily become an open-and-shut case.
but yeah... i imagine a company would weigh their options on this. if it is financially worth it or not. one thing to note, whether we like or not, bots can also potentially bring in money for a game company too. so, not only would it cost SE to take action, but they would potentially lose revenue too. i don't know what Blizzard's numbers are like, but they have a limited free-2-play model. F2P is only up to level 20, but this would still allow botters an in to bot currency/things for selling. which would in turn cover their subscriptions fee's. well, this makes it highly unlikely Blizzard would actually lose any significant amount of revenue, or any at all. while FFXIV does have a free-trial there is also, unlike WoW, a gil cap. the botter(s) could likely achieve the same effect, but it would also probably take significantly longer.
also, in that case with Blizzard... that would have been a more direct attack. in other words, Blizzard would have taken action against them for the interference of their ability to pull in revenue. and not simply for the usage of any third-party software/tool.
on another note, it is actually easy to create Terms and Conditions/Terms of Service for any domain/website owner. however, if this botting tool form the small project place you speak of is not operated for the explicit use with FFXIV... then it is unlikely they have any terms set forth expressly forbidding Square Enix's access/usage.