Looking at steady state is mostly a waste of time. A flowbench is good for examining things like different seat configurations and testing bolt on parts like throttles/carbs. Also for probing a port to find dead areas with a pitot tube.
However, many people are obsessed with steady state flow numbers, this is why heads often sell based on a cfm rating. Now it is very easy to increase the cfm substantially and loose large amounts of power, its also possible to decrease it and gain power. But that is not a rule. You could drop cfm and drop power and gain cfm and gain power. The clever bit is knowing which way it needs to go for both a given head and the required application. Racing on a tight circuit and top speed testing do not want the same motor.
There are other features to look at in the ports such as velocity profiles, shape, entry into the combustion chamber, chamber flow. Much of these last few can only be tested or observed accurately using a wet flow bench or derived from years of experience and testing.
Now of course, it does not stop there. These are just factors to bear be aware of. The cam profiles, exhaust shape/size/length, inlet shape/size/length, airbox volume, spark advance, fuel type and distribution, etc etc. It goes on and on.
The basic thing to remember is the engine is an air pump. Your torque comes from the ability to trap air with the required ideal amount of fuel for that air. The measure of this trapping is known as the compression. So of course if you fit long duration cams, you drop the dynamic compression in the midrange because the valves are held open longer and hence trap less air. But then short cams will not pump the air at high rpm as well.
The hard bit is understand the wave motions going on. Things like timing the reflected waves back from bellmouth to inlet valve and exhaust juntions and end to exhaust valve. Time these right and, in simple terms, you can gain a lot of power by supercharging the inlet or using the exhaust wave motion as a vacuum.
So in answer to the original question on the filled port. The reasons why the intake filling work so well on many bike engine in my opinion are these:-
1) You are reshaping the port and removing the flaws in the original design, or rather optimising them.
2) You increase the intake velocity which supercharges the intake charge more.
3) You increase the transient response of the motor. - a bit like fitting a smaller turbo, it spools quicker and has sharper response.
4) It requires less fuel after to make the same power.
5) You change the intake runner volume and hence its tuned length. Power curve peaks will generally shift around some.
Its a shame there aren't more people who will talk about this stuff. Its a very guarded trade though!! Black art my ass, protected art more like