LordofInfinity
Blue Mage
Well, one thing you have to take into consideration is that Goku was able to reach his full potential. Whereas Sephiroth was not able to.
Now lets say Sephiroth succeded. Became one with the life stream and became the 'God' he wanted to be, then how would Goku and Sephiroth fare. Considering before he was a god he would destroy solar systems to kill a bunch of resistance members then miraculously bring it back to destroy it again the next turn
Pitting Sephiroth against Goku in terms of the game you would have to choose a suitable time for Goku in which he hadn't realized his full potential.
I would recommend the Namek Saga Goku, because its my favourite, allowing Goku the ability to use Super Sayian but only with great difficulty and determination.
After Meteor turns Sephiroth into a God then Goku can be whatever he wants. Sephiroth would waste him.
There's a problem with your arguement, Supernova is an illusion, and although it still does damage, we can't translate the numbers accurately. And Sephiroth is a low-ranking God, as you call it. Can he create and destroy universes? We've never seen him do such things, and if AC Sephiroth is stronger than FF7 Sephiroth, then calling him God would be an overstatement.