You can change the pathing to the circle of power or to None.
None means that placement by units (say a peon type unit) will allow that unit to build units on top of or inside of other units. It also means that units can be built anywhere, not "snapped" to the grid - just like placing say mushrooms or flowers.
The Circle of Power pathing will conform the placement of the unit to the grid - like barrels and trees with small pathing, where in the editor and with pathing on you can see where the square of pathing aligns to the grid.
In either case (I believe) you still can not build a building in water or on textures that are unbuildable.
All this will do is allow units to "walk" through the buildings.
I have taken things like a mercenary camp which is more or less two walls supporting a tent like roof. After enlarging the model I used a diagonal bridge pathing. That allowed units to walk into the model from either end, but not walk through it side to side. The walking unit remained on the ground.
I have also taken units like the Centaur Tent which is more or less an awning, super sized it and used circle of power pathing, this allowed units to walk under the tent.
In both cases I placed these units in the editor and using pathing blockers to to finish off the pathing. In the case of the mercenary camp I filled in the back wall, in the case of the tent I put small pathing blockers as close to the four posts as possible. Of course this can not be done if you build a unit in the game.
You might be able to make a destructible using the Zone Indicator or Pathing Blocker model with the correct sized pathing and make a trigger that creates this "hidden" destructible when a unit is constructed. Then its a matter of figuring out the points using this trigger function:
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Destructible - Create a Summer Tree Wall at ((Position of (Constructed structure)) offset by (0.00, 0.00)) facing (Random angle) with scale 1.00 and variation 0
Where summer tree wall would be your customized destructible. Off set would be in relationship to the center of the unit. Mind using say the barrel pathing would line the destructible up with the grid.
And then you would need a trigger which would destroy or remove those destructibles when the unit dies.
If you are seeking to make a building that can be walked over you will need to place it in the editor and use the invisible platforms placing each one to where the bottom of the box is one click above the "surface" of the unit. The best way to line up the platforms to the unit is to give the unit a temporary pathing of say a barrel, place the unit, then remove all pathing via the object editor then place all of your Invisible platforms.
All moving units will walk up and over the building.
I doubt that one could make this a buildable structure since one would have to calculate every Z position for every invisible platform built. That may be possible with a perfectly flat map, but if you are dealing with a map that has variable in terrain height then your Z point will not be the same distance all over the map.