The ending was about as polarising as I expected. It was the ending I had planned since the beginning, so I wont apologise for it. If it made people stop and think then that's bonus points. I did promise a Q&A if there were questions, and there were a few, so here goes:

Weren't Erryn's actions at the end out of character? She relied on exploiting loopholes to get anything done, so isn't removing those loopholes hypocritical?

Erryn didn't want to exploit loopholes to get things done; it was simply a necessity because of the indigenous species wiping itself out due to those same loopholes. Thus it wasn't 'I should leave loopholes so that others can do what I did', but 'I should close the loopholes so others can't do what the last civilization did'.

This whole story was just a setup for An Unbound Soul?

Nope. I finished this one first before deciding what to write next. I wanted to try an isekai, and there just happened to be this ready made world lying around complete with some interesting lore and details, so a sequel just kind of happened accidentally.

Why does Erryn have so much innate knowledge that has nothing to do with dungeoning?

In story: Dungeons are artificial creations, spawned by the System which was in turn built by the original sentient races. They didn't go to the trouble of designing a package of knowledge from scratch to be downloaded into the dungeons, but used their own knowledge and common sense as the base pattern. Erryn's knowledge ended up being contaminated by their own. Out of story: Because it would have been hard to get the story going if Erryn didn't know what 'outdoors' was. (Why should she know that humans lived on the surface most of the time? A dungeon wouldn't need to care what adventurers did when they weren't in the dungeon.)

If all life is dead, how do things rot?

Any life that possessed a soul was consumed. Single celled organisms don't have souls, and thus survived. Neither do monsters of other dungeons, but the dungeons themselves did causing monster starvation and dungeon withering. Had Erryn dug far enough below the surface, and known the locations of pre-war dungeons, she could have found another stockpile of spare cores.

Of course, that raises other questions, like where's the cut off? Do plants need souls? Insects? What about the crops that Erryn grew on the surface; since they were spawned through the System, doesn't that imply they're missing their souls? If new inhabitants start eating soulless crops, are there any long term health effects? And at that point I give in. Make up your own head-canon.

Another potential explanation is that the ark site shielded its contents, and since it was supposed to be inhabitable it had ventilation. It would have protected single celled life inside it and ejected them again post apocalypse. That probably wouldn't have been enough to repopulate the whole world in the stated timescales though.

Speaking of the crops that grew on the surface, whatever happened to them? Erryn set up the experimental fields and then never looked at them again.

They grew normally, but with no-one needing to eat them and with them needing manual watering and lighting Erryn didn't see the point in continuing with them. Similarly, that dungeon stone mana leaking experiment didn't give any unexpected results, so Erryn never commented on it.

So what does platinum turn into when mana saturated? It was said earlier that it absorbed mana like gold and silver, but with higher capacity.

No idea. Erryn never got that far before the story finished, so I never had to invent anything. It isn't adamantite, which was going to come from steel and be strictly non-magical. If I had to pick something I'd probably go for Hihi'irokane.

Why did the ark spend all their time preparing for the end of the world instead of saving the existing one?

What would they do? Stop the war with force? Talking hadn't worked, so short of deposing the leaders of their respective races with violence of their own they didn't have many options. And violence was exactly what they wanted to avoid. Creating the ark and never needing it because the races made peace would have been a better outcome in their eyes than what actually happened.

Why did the ark design a system that rewarded violence when the whole point was to avoid it?

It didn't. It rewards dungeons for deaths, but the same rules don't apply to humans. (As seen when Erryn poached a human class.)

What about other dungeons? I suppose the souls of the living dungeons were destroyed by the hex bombs, but was Erryn really the only dungeon that spawned in all these years? In other continents maybe?

My map of the world doesn't have other continents. On the other hand, it also only measures about 600km across, so it's not entirely self-consistent. As for other dungeons, my lore is that spawn rate was tied to the local population, so the lack thereof pushed the spawn rate down to the minimum. I can't claim that other dungeons did spawn but sat at one floor forever, because Erryn would have found them if so.

So I'm assuming that Erryn will be the villain or at least the antagonist in the sequel, but will she be a villain villain or just an antagonist?

She doesn't consider herself a villain, and she most certainly doesn't consider herself evil. Whether an outside observer would agree with her is debatable.

Will she just be remaking the old races or will she attempt to recreate the hybrid race from this cycle as well?

Just the old ones.