Either someone swapped them, but I don't have a doubt that it was Nintendo's doing. Sometimes when they're low on parts, they'll use parts from other machines since they use the same mold. Some Gold and Black N64's have the jungle green color trays that're surrounding the contact connectors (Usually they are gray, I have a limited edition gold N64 with jungle green parts IN it).
Guitar Hero guitars have the same idea. You may notice that there is battery doors on some of the wired controllers yet there is no battery connectivity. Sometimes to meet the demand, if they find it more accessible or cheaper to use other parts, they will.