AFAIK Toady made an explicit decision to not bother with soil moving, only dealing with a tiny fraction of the stone deposits to at least make the workflow resemble real mining. In the same vein (heh) he made digging itself orders of magnitude faster than reality, so the system is overall consistent, if fictitious.
For DDA, digging effort is more representative of reality, but we don’t deal with moving soil or stone around at all. The first is a policy decision, the second is a lack of interest and implementation. If someone PRed a reasonable system where digging produces tailings that you have to move around and stash elsewhere, I’d merge it. Off the top of my head, the simplest thing that seems like it would work would be to designate where to place your tailings after digging when you start, and we would create a “pile of soil” or “pile of rock” terrain there when the digging is completed. The low-effort implementation of this would require the target area to be “flat”, and piles would not be “flat”, so if you keep digging you end up having to keep moving further away to place your soil or rock.
Likewise, we don’t have a stone layer because tunneling isn’t that useful in DDA because it takes so much effort, so it’s not even reasonable to get that far. Again, no problem adding bedrock, the initial implementation could just forbid digging entirely, with a dig through rock action requiring rather heroic levels of effort.
It looks like regolith depth is pretty variable, I was able to track this down:
From eyeballing that, it looks like most of New England has 5-10m of regolith, with up to 25m around coasts and major rivers. If we say DDA has 10m of soil deposits it skirts the issue entirely, because z-levels only extend 10m underground right now.
As for wells specifically, this gnarly search indicates that there are ~5,000 sites in Massachusetts with well depth under 30’, so I think we’re fine there.
IIRC DDA labels all underground areas as “rock”, so that’s actually backwards, but in practice we treat it like soil, so it works out 
I don’t see a pressing need for DDA to handle the soil/rock transition unless someone decided to build a df-alike in the dda engine, because in dda proper there’s just no reason to dig that much.