FOSS gamedev and creative worlds

If I save only the buildings on a map and insert the map in a singlenode-world, all buildings are ok.
But if I insert the map in a mapgen v6-world with the same parameters as the original, the buildings have holes in the walls, earth and trees on the roofs and in caves breaks water in.

You can see it on the picture: At the top in a singlenode-world in the bottom in a v6-world.


Is there a solution for the problem? I want to build a Download of Karsthafen that is not 5GB big and allows the user to walk outside the saved blocks...
At the moment, I copy all 16x16x16-Blocks-Entries in the Database with my content to the other map. The same error was with localmap-tool.

MGV6 somehow gets 'excited' by stone or desert stone and will add some dirt and trees to it even if that stone was added by a mapgen mod, a solution may be to somehow change all stone nodes used in your city and structures to identical nodes, but with different names, this is what i am forced to do in my mapgen mods.
Cavegen puts holes in everything, even mod-created structures so you could disable that in minetest.conf. Or, in 0.4.9dev add "is_ground_content = false" to the node definitions of all nodes used in your city, this will tell cavegen not to eat holes in those nodes.