I have a weird way of approaching this.
First, make a duplicate of your building and set the original's values to:
Is a Structure: False
Collision: 0
Pathing: NONE
Placement Requires: - (nothing)
Height: -X (whichever)
Ability: Locust
Movement Type: Fly/Float
The building is now an unselectable, flying unit you cannot move.
Now, it's time to cheat:
Put your duplicated structure on TOP of the one that was being lowered underground.
Set the shadow to: NONE
The duplicate building is now a dummy ON TOP of the original bulding.
Lastly, in triggers, do:
-
Animation - Set 'Unit (Duplicate)' Vertex Coloring to 100%, 100%, 100% with 1.00 alpha
to make it invisible.
You can either do this using preplaced units on the map or dynamically assign the alpha by doing some comparison-type condition which buildings are affected when X happens.
Hovering the mouse over it will select as usual.
However, there is a
major limitation/downside to this:
The model portrait will be empty when selecting a transparent unit/structure.
And: due to the edginess of this approach, you won't be able to construct buildings without handling that the same way and manually trigger the construction cycle animation to the lowered unit or something.