I order from both the HDL VTX and Valkyrie stores all the time and it puts everything in the same shopping cart.
Also order parts for both bikes from their OEM parts site and it combines the stuff in one shopping cart.
Do you mean combine the OEM parts and the "store" parts together? I agree that would be nice and more convenient but I suspect they are two different systems at HDL and that's one reason Hal hasn't combined them.
As far as the Harley parts go...Can't see how that one could be included since HDL isn't an HD dealer.