The Ford theory for domed pistons and near matching heads was probably built around several sound ideas from the engineers. It is true there would be a small increase in surface area. It is also true the dome shape could allow higher strength with less weight, but, flat pistons have proven to be plenty strong before, during, and since Ford used those with domes. So, I seriously doubt that as a reason for the change. Also, the silly theory that the domed piston "blocked flow" in a performance build is rediculous. The most likely technical reason was to increase turbulence which will result in more complete combustion.
Now to the question of testing an engine with and without flat/domed pistons: After having done hundreds and hundreds of dyno tests, of Flathead engines, I can say many of the changes we make have such a tiny, incremental value as to render them almost impossible to measure. And, building any 2 engines which produce exactly the same power is downright hard to do. So, determining why one engine might make 1 or 2 more horsepower would make a serious investigation necessary. As I have said in my book, a 1% power improvement on a stock Flathead engine is well below 1 horsepower. Being able to consistently measure that small change and then being able to assign a specific factor responsible for the 1% change is beyond the capabilities of most shops in this world.