While in the womb, a fetus has its oxygen delivered to it, and the waste products removed (all via the mother's bloodstream), so there is no reason to separate all the chambers of the heart while still in the womb.
However, once the baby is born and it is breathing, the chambers need to differentiate in order to allow the blood to reach the lungs, and the oxygenated blood and deoxygenated blood do not mix.
