Receiving a set-up is a lot different than actually being assembled. The USA Custom models were finished and ASSEMBLED in the US shop(s). The S540 and RG770 models were given final setup and detailing in the US. they were still made entirely in Japan though (aside from the IBZ/USA pickups in the 770s). Some may have received pickups in the US, some may have simply had the necks adjusted and been tuned.
The USA Customs were deemed such because there were so many options in terms of finish, inlay and electronics. Most were basic RG bodies routed for a single humbucker that were shipped over from Japan. Any additional routing, finishing, wiring and assembly were then completed in the US based on the individual order requests.
That's a far cry from being fully-assembled in Japan (like the S540s) and then being setup in the US before being sent out to dealers.
Either way, no-your guitar was NOT built in the Case Ave. custom shop. It's not a USA-made model. There's nothing "custom" about it, despite what the little plaque says. It's called MARKETING- if you put "custom" on something, then everybody who has that model of guitar will think that theirs is special.
Again, this has been discussed countless times in other threads. Try using the "Forum Search" function to find more info.