US copyright law is incredibly tricky. I don't know what it's like in Japan, or anywhere in Europe.
It's generally accepted, at least in the states, that a post-purchase EULA is not a legally binding contract. Whatever restrictions are in there are safe to ignore. As far as mods are concerned, there are three things to be concerned about:
1. Technically, S-E owns the rights to the characters. We do not have any legal right to make our own models based on these characters. Even if the polygons and textures are entirely ours, it's still no more legal than fanfiction (which is also technically less than legal in most countries). Thankfully, S-E has ignored this.
2. Technically, S-E owns the rights to the music. Not just the recordings, but the songs themselves. We do not have any legal right to make remixes of those songs, even if we use no samples and no portion of the original data. Again, S-E has looked past this.
3. Many of our mods are based on the game's original content or official promotional materials. Higher-polygon models made from the originals, upscaled backgrounds, higher-res character portraits... every time we distribute any of these, we are technically infringing on S-E's copyrights.
Here's the good news: Square-Enix knows full well this site exists. It is plenty aware of the extent of our mods. Heck, some of our members
are Square-Enix employees. In spite of all this, we have never received a cease and desist order. While it's impossible to pinpoint exactly why without any official word from S-E, it seems likely that our strict policies on piracy are a definite factor in our favor. While we use their content, we only do so in regards to the game it was originally from, and only with legal copies.
As for a well-organized Steam Workshop-esque mod download and install system... I'm fairly confident they would have no problem with that, as long as we continue to require legal copies of the original game (and as long as we don't charge; that's a big one). I'd be far more concerned about the feasibility of creating such a system (time investment, bandwidth) than about Square-Enix wanting to stop it. If anything, I would think easier access to mods would boost sales of the game.