The correct attaching hardware for the standard battery is as you show, a thin flat head bolt (stud) with a clip. The factory installed bolt, 380582-S2 5/16-18X2 in L, is documented in the body manuals, AM0001 pg 9, AM0006 pg 9 and AM0011 pg 9. The nut may have been what was questioned as it was the same as the spring shield (aka bumper mount for A-arm), 55736-S2, but a different type with a disc washer may have been found. For the heavy duty battery option, the same stud-clip as the fenders used at the rear to the front quarter was used. It's shorter. I've found many of those standard battery stud-clips and almost all were eaten away by battery acid, same for the hold down bracket. The acid effect may have prompted a replacing of the stud-clip and original nut with a carriage bolt and whatever nut was available. The battery tray looks like it was designed for a carriage bolt but for ease of assembly, the stud-clip was used.
Jim