anything is possible if you throw enough money at it.
what you’re asking would be limited by assets. in cataclysm dda, adding an asset is as simple as adding a couple lines of text and using a generic icon for it. in a 3d engine, it requires modeling and texturing a world item as well as a representative icon. you also have to deal with texture memory limits based on the game engine.
the game 7 days to die might scratch your itch for a 3d crafting zombie survival game. it’s set in a random voxel world and you can customize it to your hearts content.
now as a side note, i could see this game being ported over to unity using 2d mode and tiles.