IMHO there are hordes of employees at Harley stores who shouldn't have those jobs. I don't expect that to change anytime soon.
A good parts counter person should definitely know by now that the CVO's all have supplemental manuals as well as the full manual for the particular bike "family". But we can't automatically assume everyone who buys a manual has actually talked to a counter person and told that person exactly what bike they are buying a manual for. Many places have a display rack that has manuals you can pick up and take directly to the cashier. Other people buy their manuals online from one of the 20% discount places. But yes, I totally agree if you go to a dealership parts counter and tell the person you want the shop manual for a CVO, that person should know that a CVO has two shop manuals, the main one and the CVO supplement. They should also know there is a CVO specific parts manual, and then the Electrical and Diagnostic Manual for the bike family, which I personally think is a must have item for anyone who wants to know how all the electrical stuff is supposed to work on these bikes and how to troubleshoot those items.
Jerry