There are many things to think about in terms of the final scenes in FF1, such as the fact that Garland is Chaos, and yet in Dissidia, they are separate entities.
I always like the way they close out the story by closing out the time loop, but leave the question of how the evil was born in the first place.

Time travel/time loops are difficult to work with. Here's my theory. In Final Fantasy a time loop was running where Garland would be defeated by the warriors of light in the present then sent 2000 years into the past by the power of the four fiends. The warriors of light travel to the past where Garland transforms into Chaos. Garland/Chaos then defeats the warriors of light and sends the four fiends to the present where they can again send Garland to the past.

My assumption is that Chaos, being a God of sorts (at least in Dissidia), would've have lived those 2000 years up to and past the point where the time loop starts over. So even though Chaos and Garland are one and the same, during Garland's life in the present they existed as two separate entities.

In other words, once the warriors of light have been defeated and the four fiends are sent into the future (present) Chaos begins to exist independent of the time loop.

Just a bit of speculation, I could be way off base.