Well we knew already how the Super Mutants in Fallout 76 were explained but reading it again still pisses me as a Fallout 1 and 2 fan of a lot.
As for the Ghost People clones, they are called Mole miners;
https://fallout.wikia.com/wiki/Mole_miner
I remember from the Van Buren documents that the player was suppose to meet the Mole People; but these would be revealed to be just crazy survivalists who had dug an extended network of tunnels underneath their settlement for defense.
Still better than a dedicated monster type that only exists to be shot.
From the holodisc "Formation of the Brotherhood of Steel"
"
Scribe: Appalachia online, Captain.
Roger Maxson: I know most of you love America. The good old red, white, and blue. But those of us that served at
Mariposa know something. America failed. Not because its citizens, who lived clean lives filled with hardship in a never ending war. And certainly not because of its fighting men and women. God bless them. No, its leaders failed us. Senators, Generals, Presidents, all those bastards. Their failure almost destroyed all mankind. But I look around here and I see survivors. People too stubborn, too damned ornery to die. We've fought and we've endured and finally we have a small patch of safety. But having a home isn't enough. We need something more. What we need is... purpose. But we cannot look to the America of old for that purpose. We have to build our own. So tonight, as we break bread together, let us forge together something new. Something strong. Something we can be proud of. Something we can build upon. We'll preserve what's best of what's come before and use it. And one day, we will reclaim what was lost. Let us forge a
Brotherhood of Steel."
I know it technically doesn't contradict Fallout 1 but Maxson never brought up the US government up like this, let alone seeking to unite people to forge something new (the BOS) with the idea of having that take the placed of the United States.