Second, I think you answered your own question. Bekeart served as Colt rep, distributor, and wholesaler. He likely sent the gun on to your grandfather's local dealer, where it was picked up. Not all that is necessarily reflected in the shipping ledgers at Colt.
PS: An additional thought as to why the special order in the first place, rather than a local purchase: I’m fairly certain that’s due to the caliber. The .38/40 was a niche load and not very popular any more in the 1920s compared to the bigger bores in the New Service; maybe your grandfather wanted the caliber because he also had a rifle in it, but could not find one locally.