Yes, in the old days when bicycles were 'hand built', it would have been standard practice to file the cotter pins to suit each assembly. Another problem us Douglas owners have is that Mr Douglas did not use the same standard as BSA, Triumph, Etc. with regard to the distance from the kickstart shaft hole to the cotter pin hole, so invariably, 'standard cotters' have too large a flat for our purposes.
Regards,
Eddie.