I don't really want to get into the "But they're dwarves, not humans!" argument. It just strikes me as funny that Toady went to the trouble to research geology to get a moderately realistic world gen happening. The stones appear in areas where they would naturally be found, close to stones which they are naturally found close to.
But then, I guess there's tons of different trees, too, and no real need for them either.
Well, theoretically those should have different material values and uses, too. Some should be better at producing charcoal than others, for example.
So I wouldn't get overly concerned about accurately modeling things like lead poisoning or mercury poisoning. How do you know dwarves are even susceptible to those? It's just as good arguing they are as they aren't. Although I suppose humans using them would be in bad shape in the long run.
It's not about "accuracy" or "reality" per se, as the goal is to model a compelling fantasy world. However, we don't have to argue about it in any case -- poisons and poison resistance will be in the raws next version, so we'll know what canonical dwarves are susceptible to, etc.
To address the OP's questions:
The mica greenhouse thing is definitely impossible right now, and will not be possible anytime soon, mainly because it requires implementation of a LOT of new stuff, such as the effects of light on crop yields. Even the next version with its gigantic lists of material properties will probably not include opacity/transparency.
Contact poisons are slated for the next version, but the notion of "contact" will probably be a little restricted. Standing in the same tile as a contact poison probably won't have any effect -- you'd have to get spattered or dusted with it. Hmm, now the game just needs to make that happen more often.
Woah, slow down. You're conflating two different kinds of "poison". Yes, "poison" will be modeled better. I don't think that's going to extend to something like heavy metal poisoning, which generally takes years and years to build up before it manifests symptoms. If you ate bread baked from flour milled from a cinnabar millstone, you would be fine. If you kept eating it for years, eventually you would not be fine. If you've ever had tuna (or any fish, really), you've ingested some mercury. You're basically talking about pollution, not "poison".
If we're going to talk about modeling pollution, the first thing we need to talk about is my legendary furnace operator who should have developed lung cancer a long time ago; the same is probably true of my miners. And where does all the leftover slurry from smelting and forging go?
I agree that DF is about a "compelling fantasy world". But I don't think pollution is part of that world. Material values and differences ARE a part of that world: I shouldn't be able to build a room out of soap and fill it with magma forever. But really, do you want to deal with building an OSHA-approved fort? Because that's basically what this would require.
More importantly, there are an infinite number of things Toady can add and only finite time. I don't see this being a priority for a long time, if ever.