So I just stumbled upon this when setting up the Elf race.
Apparently, you can still build buildings that don't have a tile design. They will take up 0 tiles, and you can't ever delete them (so careful with those upkeep costs!).
All it takes is to get the user to select the building, then click the Build button, or click the map like he was really placing a tile.
Anyway, I hope this can help some people who are trying to reduce the amount and size of cities, without taking away the possibility to actually upgrade them.
