I'm using Fluent in these simulations.
A Y will be more efficient than a T for airflow in a steady state, that's correct.
Keep in mind that with three cylinders to a plenum, there is a pretty much constant flow of air into the plenum when the engine is kept at a constant speed. There is always a cylinder pulling air. The pulses that influence secondary pressure waves are important, but they are secondary in nature so the influence on flow is on a much lower order than the primary vacuum pulled by the cylinders themselves.
Here are three more simulations varying on the one I posted earlier. The first one just adds a sloped wedge to the original T. The second adds a large radius to the T junction and the last one combines the radius with the wedge.
The volume flow rate results show that the T and T with wedge have almost identical flow rates. The radius-ed T with and without the wedge are both almost the same flow rates but are about 30% greater than the standard T.