SeeD stands for SeeD. The name comes from a paradoxical timeloop, and Squall- who told Edea the name, didn't know what it meant.
That's pretty confusing right there, the whole timeloop thing, I mean when he went back in time at the end. It's like, if Squall told her the name, and then went back in time again, the whole thing just like plays itself over and over again lol. But how can there be 2 Squalls at the same time? And if he did go back in time and told her that, where did the name originate from, it must have came from somewhere! So I agree with the theory about SeeD, and Garden. And perhaps the D in SeeD was simply for it to stand out, because if you were reading through text and saw "Seed", it wouldn't stand out as much. Or maybe we are overlooking it, and it is simply a typographical error, and they decided to keep it because it looks cool lol.