How do we know how much Uranium was in any given sample when it was deposited?
The chemistry of lead is very different from that of uranium and thorium. There are key kinds of rock that could not possibly have been formed with even the smallest amount of primordial lead. The lithophilic nature of uranium and thorium means that those same kinds of rock could easily have readily accepted primordial uranium or thorium.

Any lead in those kinds of rocks must necessarily be the result of decay of uranium or thorium after the rock formed.