the gauss rifle does more damage per shot which is what the devs were probably thinking about as well as the fact that its a story so not all of it has to be logical
he couldnt have made it what would he have used to make it he says to use it as a replacement (correct me if im wrong) and also if he made it then why would he immideatly create mods for it then code them into the vending machines then restrict them an scatter the access codes around the area
"wish i..still had that damn holorifle *inhale* spent forever makeing it..need to find it once this all done" - Father ellijah's radio signal
You guys know he didn't give it you, right? Remember he says something about contacting through your pipboy? Dog may have given it to you, or it may have been left there. He made it, but how you got it is speculation. But he is trapped, which is why he only contacts you through your pipboy and the hologram.
I like the idea of the weapons and armor of the dlc to be in the vending machine. maybe it could poop out the automatic rifle and the holorifle in parts so with enough repair and science you can make them.