Again people that play 100% legit are screwed because SE can't get their ***straight. Very sad.
Firstly, if you don't like Linkshell Community (you shouldn't) you (or someone passionate enough) should make a petition to get it changed. For players who don't play on PC, or do but don't trust windower or guildwork for whatever reason you may have (breaking of ToS should be your major concern), then you shouldn't wait for SE to give you an update when they have no plans to do so.
Either ask for the Linkshell Community website to be updated and support what other community websites offer and more, or have them integrate Linkshell Community into the Official Forums so they don't have to support both sites (like they are even supporting linkshell community~).
Using Windower and/or Guildwork is breaking the ToS, you can't ignore this fact, but you also can't ignore the influence it has had on the game. Many of the updates you have had the past 5 years were influenced by Windower. There are over a dozen updates that come to my mind right now that were inspired by what Windower has given to the community.
If you enjoy the vanilla experience of FFXI then good for you, many feel it is limiting though. That does not mean it's okay to just break the ToS without a second thought, it just means that it has become necessary for many to break the ToS to even enjoy the game, and for the large majority of players that wasn't even enough and have long since quit the game for good.
Anyone can see how this game has aged, and I know SE is giving us updates, very very slowly, to upgraded how our UI looks, and we will be getting a brand new UI soon (PC only). Unless you haven't played any other game in your life, FFXI would look very old and unappealing to you today. People want things fixed, to enhance the game, and since SE won't give an unfair advantage to one platform over another (they shouldn't), we are forced to break the ToS to do so ourselves.
I believe SE has accepted this on the inside, because when Windower or Guildwork receives an update, like this one, it improves the game experience. We are able to enjoy the game, outside of the game, having our profile be updated on community websites and interact with other players from other servers, all at no cost for SE.
Yes, Windower opens up exploits to gain an unfair advantage over players, some more than others. Using official plugins, besides spellcast or autoexec, will net you a slight advantage, but they are more UI enhancements than anything. Delving into Spellcast or Autoexec will break the chains that held you down for years on enhancing your macros the way they should be by now. If you're knowledgeable enough in spellcast or autoexec you can gain a far too great advantage over other players, but using it in it's most basic form is no different than what your macros do, except you have more lines. Then there are unsupported 3rd party programs that automate the game for you, that aren't supported by Windower, that give players a much too great advantage over others.
Whatever the case may be, if you use Windower or Guildwork you are breaking the ToS, but many don't care. It's their money, and if you want to play vanilla mode you can, if you want to enhance your game and modernize it a bit then you can, though you might run the risk of getting in trouble for it (very unlikely).
However, players should not be forced to break the ToS if they want their community profiles updated on websites, and this is where SE is to blame for this like you said. If we really want SE to support these things, we need to ask for them, and we need to push for them. They aren't going to update Linkshell Community anytime soon, probably ever, so if you really want something like this updated so players who don't play PC or use Windower/Guildwork can have updates to community websites, then you really should do something about it instead of being ignored year after year.