I can't say that there are any great advantages to stacked ports.There are times when I think that it was an idea that should have never gotten past the cocktail napkin after a 3 martini lunch. But stacked ports are what we have and what makes a Y-Block a Y-Block in my mind. I can remember when any other design looked strange to me.From an air flow stand point the biggest problem is that the lower must rise from near the deck surface to a reasonable height of around 1" in order to make a well shaped turn toward the back of the valve. The air must approach the back of the valve at close the valve angle of 18 degrees. Some early Y-Block heads have a lower port that follows a gentle arc and approach the valve nearly flat. This is what limits the lower port air flow in heads such as the ECZ-C.
A problem arises in trying to make the lower port rise. It is under the upper port so only so much can be done before the divider is breached. This is why the upper ports in ECZ-G heads rises just passed the gasket surface, to make room for the lower port. In the case of the aluminum head we decided to design a lower port with as close to the shape we wanted as possible and fit an upper around it. Over it might be a better term.
In actual air flow numbers the lower port flows more than the upper to .450" lift. From that point on the upper is better. This is interesting to me because everyones answer to designing a new head is to raise the ports. But with the same gasket opening, valve and valve job the lower is better over much of the flow curve. Perhaps if the upper port was not compromised to fit around the lower it would be better.
I think that stacked ports fit into the Ford engineers plan for the engine. I believe that they intentionally put turns with sharp edges in the ports to increase turbulance, thereby keeping the mixture homogenous. Having the ports wide and low forced them to turn more than a side-by-side port head. Again the turns have corners that are sharper that they need to be. These turns ensured that the majority of the flow would pass by one side of the valve guide. This produced a great deal of swirl in the chamber. The chamber being offset to the bore increased squish area to increase mixture motion during ignition. Even the valve seats were recessed intentionally to produce turbulance as the mixture entered the chamber. Speed-o-motive found that recessed seats work well in nitrous oxide engines and probably didn't realize that Ford did it 55 years ago and were following Ricardo's findings from nearly 90 years ago.
I think that the engineers did all this in an effort to reduce detonation and improve fuel economy. Unfortunately, at high RPM these turns hurt the power.
Due to the interaction of the ports with the stacked design I do feel there is a definite wall in regards to airflow and horsepower. There are still avenues to explore that would help straighten the ports and lead to increased power but there is only so much that can be done with the limited time and budgets of Y-Block development.