Yeah I've done that, junctioned at all he's ridiculously easy. 1st time it's 1v1 anyway, the last time you can draw aura making it a sinch. And the other two times he does about 300-1000 if you've junctioned to life you'll have about 5000 life and to a lot more damage than he does every hit.
Back on subject as someone said whoever you're playing as wins:
You're Squall to make the storyline continue you have to beat seifer.
You're Seifer I assume the same would be true for you.
But Squall with 2 companions beat 4 forms of Ultimecia/Griever and all 8 of her stronger guardians. The best seifer has done is defeat odin, but he is just another of guardians- and the weaker than the others. You beat his mistress and him, Squall wins
