Sinking occurs only, when the weight of the ship and cargo exceeds the available buoyancy of the hull. In the Estonia AIUI this was 18,000 tonnes so loading 40,000 tonnes of metal on to the superstructure is just silly and it would sink like a stone.
However, it could handle the 2,000 tonnes ingress of water because with its tonnage of 15.5 tonnes with maximum allowed cargo and passengers (it was only half occupied 28.9.1994) if it capsized due to imbalance, it would simply float upside down.
Try it. Get an empty plastic bottle. Fill up a kitchen sink or bath. Throw the bottle in. It floats of course. Now half fill it with [very heavy] water and throw it in. Guess what it still floats! Now fill it completely with water. It immediately sinks. Why? It is all to do with displacement of air.
If the car deck was never violently filled with sea water nor breached its doors with a 9cm water barrier, then there is no way the vessel would have sunk.
So the JAIC had to assume it breached the doors, smashed windows on the next deck up and this displacement of air by very heavy water caused the sinking. However, it would still take time for it to displace all of the air in each of the cabins.
However, Kurm's investigators found the car deck doors shut and intact.