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Very interesting that they were getting lead exposure like that from living in caves near lead deposits or drinking contaminated water. It perhaps says something about human history that we always seem to end up in that exact situation over and over again - from the roman empire to modern USA, all have had problems with lead exposure.
Lead is perfectly natrual - early pewter itself can give enough to be outright lethal. Nature is full of well hidden dangers.

It brings to mind a thing about ancients - occasionally they would build a city in a location that would be very bad if they had sufficient geology to know that say a massive eruption would eventually kill them all or the whole shelf will eventually fall off into the sea. Their neighbors come across the their utter destruction and wonder what they did to anger the gods into eradicating them completely or if they already had horrible relations figured they totally deserved it. It brings to mind a dark joke that the gods really hate bad geology in settlement location.

I am reminded of one Minioan city and what archaeological evidence suggested - usually one villainizes their foes. They had their evil downplayed - there was evidence they would demand adolescent boys and girls for human sacrifice from their subjects. A gas erruption killed many of them shortly before an invading army of their revolting subjects arrived and turned what would have probably been a battle they would lose to one they won by showing up.

Compared to the minotaur myth where a king's love of beauty of a bull he promised to sacrifice in honor of a god who gave him the sign of his worth to rule they are downright sympathetic and even their crimes were justified and made tragic even with the added monster and bestiality.

Is there such a thing as good geology when it comes to this sort of thing? Or are we essentially makeing a tradeoff here that lead etc is less bad than say in the next valley where its full of arsenic etc?
Good geology would be knowing to stay away from the tell tale danger signs and recognize the area as best unbuilt. Given that it would also require knowing all about the chemistry and dangers which may be extraordinarily subtle and they likely weren't even at protochemistry it is essentially life being grossly unfair to them.

Even Dwarf Fortress fans would object to colorless odorless gas occasionally killing entire settlements with no way to detect it. Especially when one counter - torches for burning methane can itself lead to carbon monoxide another toxic one in addition to explosion risk. To add insult to injury radon also kills and doesn't cause tiring or burn and the player can actually know that these exist. Those sort of impossible to know before dangers happened a lot - like early days of radiation research. Let alone retrospect foreseeables like "should have known inhaling any smoke would be bad for your lungs".

>Even Dwarf Fortress fans would object to colorless odorless gas occasionally killing entire settlements with no way to detect it.

I'm sorry, but airlocks and decontamination chambers are a key to any fortress. :)

For one, having enough iodine in the soil was important before we started fortifying our food with it.