I swapped the cams when I was adjusting valve clearances, so I had the cams out anyway. My conclusion was based on my experience riding the bike before and after.
As far as quantifying the gains, I don't have a before and after dyno, but can offer this:
-A lower lift height on an intake valve reduces the maximum amount of gas that can flow into the cylinder for a given duration.
-For a given intake lift height, more duration increases the maximum amount of gas than can flow into the cylinder.
-Valve overlap makes it possible for an intake charge to be higher than the maximum obtainable by the swept volume of the cylinder alone (which is the most you'll get on the later model year Honda cams since they don't have valve overlap).
I don't understand your comment about "custom ground cams with more lift and duration". I did install cams with more lift and duration; I just didn't have them custom ground.
Honda clearly changed their cam design to meet emissions requirements. There is no other explanation.