Think about the planet early formation. It would've had a single crust at the begin and then rain will fall and be captured in that layer and then more layers of crust would form on top of that previous layer which now stores the water.
Could it of have rained more in one part of the crust then the other parts, yes as it still rains more in some parts of the world compared to others, but that won't mean other parts received no rain at all especially we are talking billions of years here also. We are at our final layer the continents with water surrounding it, I would assume it's the same for the lower layers with shelfs of continents with water surrounding it looooooool. Some probably more deeper then others but their still damn deep all around cause were talking billions of years of rain pouring down.