i had the same issue, i started play FFXIV way early than Steam version was announced, i got my copy at SQEX Store. When Steam version released i got a copy there and it was a waste of money, i tried to contact the support and they said me it was impossible to apply Steam options in account or transfer my character. i just gave up, they are not going to change this politics ( i don't know why that kind of stuff is even there to begin with ).