I forgot to mention that about Amaurot, too. I noticed that - I went back to grab a quest there, and was stunned to see it still "standing". Squeenix has shown they don't mind making areas look one way before x happens and they look different - I'd be surprised if they got lazy with Amaurot. They could have easily just made it shattered hulks of towers - they obviously had that resource ready (from the ones you see as part of the Odon's Cups).
I'm wondering if it's not possible that he intentionally set everything up to have the WoL "destroy" him. There's a myriad of reasons I can think of where this might be a good thing, though plenty are far-fetched. My main one however, is this: maybe the way we did it flushed his mind of the tempering of Zodiark, like you mention. The only evidence I have is that, while a lot of what he says right before the Amaurot dungeon is unlocked is horrible and cruel... the expression on his face is *hurt*. I'm no psychologist or anything of the sort, but Squeenix modeled his face to look that way for a reason, and it's not pure anger, or a sneer on his face. It's "this hurts me to say this". Also, we know that the only way to "cure" tempering is through death - but Zodiark's tempering isn't the normal type of tempering, is it? At least, it doesn't seem to me. And either way, Emet - or any other Ascian - isn't just some person. So while a tempered Ascian may "die" (not a permanent death), it may not remove the tempering. But the WoL -used- their surplus of Light against Emet, and... afterwards, didn't Alisae, or was it Y'shtola, talk about about the WoL had a surplus of Light vs Emet's surplus of Dark? I'm going to post this, go rewatch the cutscenes, and then edit with a better argument for this. I've got a thought and I don't know if any of this makes any sense but here we are.
Sorry, as I said, I only watched the cutscene once (and I'm about to go remedy that). Still, my main point is: the auracite didn't remain in his body, we hit him with a "blade of light" only after he had removed the biggest spear, and Emet's physical body (as far as I know) was still -there- in the, uh, people space. It was not contained in any of the auracite. ...I think.