''It all began with a stone, Or so the legend says. In ages past, a sentient jewel, enormous and beautiful banished the darkness."

Oh, wait. Wrong game. Oddly appropriate, though... XD

One issue I see with putting too much stock in the Twelve as founding deities, though, is that they are not universally recognized as gods. Folks outside of Eorzea have never heard of them, short of their interactions with Eorzeans. The Heavensturn emissaries clearly consider them to be quaint local customs. Eorzea, while highly relevant to us as players, is just one continent among presumably many.

I think that it's possible - likely, even - that the Twelve were ordinary heroes in the distant past who were elevated to deities. Elevated either through myth and legend, or possibly literally with them being summoned as Primals at some point. Or both. While the Twelve were doubtless a very important part of Eorzea's past, I don't think we have enough info to deduce that they were an important part of the WORLD'S past.