Strictly speaking you pay stamp duty on the value of the property at the time of signing the contract. Prior to construction commencing, that's only on the land component.
In many appartment buildings, the land value of the individual units is quite low, so the stamp duty is minimal.
Keep in mind though, the building depreciates (goes down in value over time), whilst the land becomes more scares, so it goes up in value. Properties with the best capital growth tend to be those with a high land value.