Hi jimp,
I can see your point somewhat.I don't think a Harley would be as "efficient" as a sport bike when it comes to streamline design or H.P. per LB. of bike. But that is like compairing apples and oranges.
I agree with naitram in that there are many types of CVO owners and they all have different riding styles and plans to personalize their bikes.
I am comming from an 80" Evo Fatboy and have no immediate plans to alter the 103" engine I now have. But that doesn't mean in a few years when I get used to it and everyone else has a 103 or bigger I might feel the 103" needs some work or I may trade up.

From my reading up on the factory 103" from this site and magazines I do believe the HD factory has to detune the engine to meet government regulations as well as trying to cut cost in manufacturing.
So I am sure many of the folks who modify their motor are trying to make them run more efficienty and get the power that is hidden in the engine.In some cases to make it more dependable by eliminating the weak spots such as mentioned by Fired00d.
I just hope the increased EPA regulations and the "noise police" types don't hurt the performance and aftermarket business for those who choose to modify their engines.