"Tékumel has spawned four professionally-published roleplaying games over the course of the years:
Empire of the Petal Throne, published in 1975 as a boxed set by TSR, Inc. and reprinted later as a single book by Different Worlds Publications in 1987.
Swords & Glory, published in 1983/4 in two volumes by Gamescience.
Gardasiyal: Adventures in Tekumel, published in 1994 by Theater of the Mind Enterprises.
Tekumel: Empire of the Petal Throne, published in 2005 by Guardians of Order."
With 1 billion years we could be talking about 8 different civilizations where humanity moved on and settled other planets or even galaxies. I'm pretty sure one of those former civilizations is a galactic federation of some sort. Another former civilization could have "ascended" or gone to other dimensions. And it's possible that something like rats could have evolved and become a great civilization themselves.
While I'm not in the market for a new system explicitly tied to a setting, Numenera sounds pretty cool.
As for the 'billion years' thing... Gene Wolfe had the sun fat and red in his "Book of the New Sun" novels. They are, in short, masterpieces. If that was okay with Gene, it's okay with me.
Scientific accuracy only matters in fiction that explicitly makes it matter. Highly romanticized science fantasy full of science-wizards does not, as far I can tell, make any strong claims about accuracy. It does stake out a claim to the Dying Earth subgenre and can be judged accordingly.
I don't want to reveal too much, but perhaps your definition of "great civilization" differs from what Monte is using in the context of this setting. If your civilization didn't get to transhumanism and terraforming, perhaps it didn't count?
This is Monte's thing and I'm sure he knows what he'd like to talk about and when. I don't know if what you're talking about is an "overall theme," but (like the Dying Earth books) there's definitely an element of "great civilizations have risen and fallen in the past, leaving behind sites and artifacts."
I probably should stop talking now, I don't want to post spoilers for anything Monte plans to talk about later.