I'll be damned!!
I just went out and looked at the engine on my FXR2 and there is a '4' stamped into the 5th cooling fin on it also. A little harder to see under the powdercoating, but it's there.
I also don't know if the MOCO does anytning special to the CVO engines, but I have a strong suspicion that, if nothing else, the cherry-pick the motoros for use in the CVO bikes. In 2004 my brother-in-law bought a S.E. ElectraGlide with the 103" engine. I bought a new UltraClassic at the same time and had the dealer install a factory 103" kit before delivery. All I know is that his bike would flat walk away from mine at any speed. He weighs 60lbs more than me, so that zeroed out the difference of the weight of the bikes. So I kinda believe that the Factory either picks the best engines off the line, or hand tweaks the motors that are used in the CVO's. I'll certainly bet this was the cas for the early CVO bikes like our FXRs.