The Thirteenth's time line flow (POSSIBLE SPOILERS)

[Enkidoh]

Which I guess brings up the question on how well did the unsundered understand the time difference between shards and what not? As Emet seemed perplexed about how G'Raha managed to turn the Crystal Tower into a time machine.

That was more just Emet's arrogance about how he was technically the tower's real creator and so didn't think it was even possible, something he created being repurposed in ways he never believed could be done, (he outright says "I know every one of this tower's secrets"), and thus, could not comprehend exactly how these 'lesser creatures' managed to turn it into a machine that could transcended time and space.

He was an Unsundered Ancient, one of the last surviving members of that "pinnacle of civilization", who had the very powers of creation at his fingertips... and yet... had no idea how a big lump of crystal could be sent across Shards back in time, and that fact would have frustrated him to no end (hence why he shanghaied G'raha away, it wasn't just bait to lure us to Amaurot, but to try and learn from G'raha exactly how he did it, the secret how the Crystal Tower became the Crystal TARDIS.).

Of course, he never did find that secret - we defeated Emet before he could wrest that secret from G'raha, and besides, G'raha wasn't talking anyway.

It had nothing to do with the time difference between the Shards, that was just a handwave by the writing team to explain away potential contradictions as to how long ago the Flood of Light was stopped and the length of time G'raha could establish himself in the First as the Crystal Exarch not 'lining up with the current setting', so it's really something that shouldn't be thought about too much.