No.
Also there is no way to create an "underground-only" POI. You can make a POI that has only underground stuff, but the surface itself will also be part of the POI. It's surface will not fit into the generated landscape (or will be blended in like known from "normal" POIs).
Imho, you can see this with the vanilla "well-bunker" POI. There is only a well on the surface and next to it theres nothing and the surface is absolutely flat. Underground (going down the well) there is relatively large bunker, but sind POIs can not overlap, also not over oder under each other, everything next to it is as far away as the underground part is in size.
Afaik a POI has no height, it's always from bedrock to the sky. You can easily see this if you dig a tunnel far blow a poi. If the POI is reset by a trader quest, also the undergound structure respawns and you tunnel is closed again. And that's why you can't place POIs overlapping or even fully under or above each other.