I don't think I'm going to explain this really well, but poppet valves have a completely different function than the throttle valve. The poppets (usually just called "valves" are driven by the camshaft, which is geared to the crankshaft at a 1:2 ratio. The faster the engine goes, the faster the valves open and close. They are controlled by the engine speed. The engine speed is controlled by the throttle.
The throttle opening is controlled by the operator of the vehicle through linkage to the accelerator pedal. All else being equal, the more you open the throttle, the faster the engine runs. You could say that the valves determine the maximum amount of fuel and air that pass through the engine, but ignoring certain alleged Toyota problems, you don't always want it to run at maximum speed. The throttle valve allows you to decide how much of the engine potential you want to use.