He said he watched a supernova, a process during which a lot the heavier elements (or building blocks of the universe as he calls them) are created. So he wasn't talking about the creation of the universe itself and the timing should still be ok.
“In all your travels, have you ever seen a star go supernova? ...
I have. I saw a star explode and send out the building blocks of the Universe. Other stars, other planets and eventually other life. A supernova! Creation itself! I was there. I wanted to see it and be part of the moment. And you know how I perceived one of the most glorious events in the universe? With these ridiculous gelatinous orbs in my skull! With eyes designed to perceive only a tiny fraction of the EM spectrum. With ears designed only to hear vibrations in the air. ...
I don't want to be human! I want to see gamma rays! I want to hear X-rays! And I want to - I want to smell dark matter! Do you see the absurdity of what I am? I can't even express these things properly because I have to - I have to conceptualize complex ideas in this stupid limiting spoken language! But I know I want to reach out with something other than these prehensile paws! And feel the wind of a supernova flowing over me! I'm a machine! And I can know much more! I can experience so much more. But I'm trapped in this absurd body! And why? Because my five creators thought that God wanted it that way!”
It was almost certainly the same one, supernovas are rare events, in real life nearly all supernovae that we've observed have been in other galaxies, the last one in the Milky Way happened in the 1670s. So the chances of there being two separate events (especially considering how everything is connected in BSG) are very slim!
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