I've seen reports of behaviors similar to this, where trees grow in the sky and then fall when they realize they have no support (the Coyote and Roadrunner syndrome). I've heard at least some of these cases have been caused by caving in the ground the trees grew on originally, and somehow the trees aren't notified they should no longer be there.
I would try to locate where this happens and then build a solid wall up to and including the tiles the trees fall from. It might even be possible to dismantle the wall when these tiles have been notified they no longer support growth.
An alternative, which is well within your capacity given what you've already done, is to build a floor to support these bewildered trees, but I have no idea what will happen when they form.
A third alternative could be to use DFHack to modify the material in the tiles (which would probably cause a cave-in as the cobaltite or silt you created starts to fall) hoping that would clear the tile's memory of tree support.
Note that none of the suggestions above have been tested, to my knowledge.
I have no reasonable explanation for why this happens. However, if this is the same fortress you shared earlier, I noticed in my recreation of it (new world with the same seed) and a 3*3 embark, that a location some 10 tiles outside of the evil area, to the east, generated fog on top of a construction I made to cave-in kill a visiting titan, i.e. at 1 level above ground level. This indicates this embark is one of those where there are different biomes at different Z levels, and I wouldn't consider it impossible that there are some biome shearing over the evil part as well.
It definitely has "biome shearing", which is bizarre. A tanner's shop on floor 2 in the good region is safe. One on floor 3 leads to the dead walking. What?
Since the original post, I've also seen persimmon trees growing in mid-air as I've just let it happen. The point seems to be that they're supported from above by other trees, so they don't fall. Cave-ins seem to be less now but still come, as I've just let the trees grow.
I think I will obsidianize the area up to z+1 as that is where the tree trunks are growing. Then if they still want to grow on obsidian, fine, I'll have the world's coolest tree farm. We'll see if it works.
Focusing on my GCS breeding program now (caught 2 in my cavern spawn trap), so this may have to wait just a bit.
Never seen it happen on the surface though. You say things periodically collapse over there for no reason: was there ever a time when it did not happen and did you ever engineer a cave in in the area that would land in water?
The area where this is happening used to be a 1 z-level high clay hill which I leveled by carving up ramps after chopping down the trees on top. No cave-ins or if there were, such as one tile during the leveling. No water is below. Mud is not visible in mid-air.
This seems a bit unrealistic. I have a backup save for a bug report, but DFFD seems to be in trolling mode, "uploading" for 1 hour then popping up "server error", so another time I guess.
Edit: also, come to think of it, I leveled most of the map the same way, with no tree-related issues. And it was all forest. So something unusual happened here, but I didn't notice anything.