Basically all correct Terry.
Mostly all stock systems are California (CARB) Compliant.
Many aftermarket pipes are not and will fail a California inspection.
But if one doesn't live in California......one can do some pretty neat stuff.

Now, living in Pennsylvania, the bike's are inspected yearly, but my '95 HD has been "grandfathered" into the older category of not requiring an emissions test.
For those guys living in Florida, there is no emissions test and I don't even think there is an annual inspection, so you can pretty much do what you want.
Everything varies by state.

The Thunderheader exhaust on my HD is not CARB compliant.
The air system has been reworked.
The carb has been replaced and has been re-jetted.
She's been dyno'd & tweaked repeatedly until her 80 cu inch (1310 cc) Evo motor produced 80 hp and that was in 2009. Not bad for a '95 HD.
Without adding a blower, that's the best she's gonna do.

I'm sure that the F6B could be tweaked for more horsepower with an aftermarket exhaust, but I do not know what can be done to the air intake, again, short of adding a blower (turbo or supercharger).
The intake maybe "open" enough to lend to some tweaking of the exhaust system and chip, but with most F6Bs still under warranty, I don't think anyone has gone to a "total performance" upgrade - yet.

Will be VERY cool when it happens though.....