The applications are sent to NCC for the background check. The investigators are there. The presiding judge at the superior court in your county of residence is the one who approves it. Even if they accept it, the NCC prothonotary would probably put your app in a big batch up there and send it to the investigators. That is, if they accept it from somebody who does not reside in NCC. If they do tell you to file in your own county, then a trip all the way up there would be for nothing and it could take you even longer to get your permit.
Maybe not, but that's the way I see it.