Steam wasn't a "platform" until Heavensward was released in 2015. There was no distinction at all until that point and no way for anyone to know it was a completely separate licence.
Sorry, but with that statement you've demonstrated you don't understand the problem. It is not possible to put a Windows licence AND a Steam licence on the same service account. If it was then people would have a workaround and could go down that route, but right now they can't. Square Enix is the only one who can fix this.
If you want to quote the licence agreement you should probably should read it first:
https://store.steampowered.com/subscriber_agreement/
Even right now it's not a requirement from Steam so as to why SE is forcing this remains unknown.