I would like to point out something called the cannon ending. Any assumption on someone NOT being capable of appearing due to how you played the game is utterly false.
Fallout 1's Cannon ending is good karmic hero ending, which is quite clear when playing fallout 2. As Marcus in New Vegas mentions traveling with a tribal and considers him a friend we can assume a good karmic ending for fallout 2. If we follow the tradition the good ending of fallout 3 will probably be a heroic lone wanderer.
Games rarely go for the darkside ending.
Now here's an idea maybe it will be Col Autumn, after all you never hear what happened to him if you let him go in fallout 3 and he could have escaped through the Taft Tunnel just like you did.
Serious answer: If true, my real money would go to Either Elder Lyons or Sarah Lyons. Time for the elder to face the music concerning his actions in the Capital Wasteland.
What music? the Western Brotherhood is in no condition to recall Elder Lyon's and Elder Lyon's would be far to busy in the aftermath of the Enclave war to concern himself with returning. Its also apparent the east and west coast had some means of communication before they cut ties. With all that enclave tech it be more likely the West coast would be kissing Lyon's butt.
They arn't underground. If they were then NCR's economy would be doing great.
Yes they are all underground, all the BoS bases in the west are underground bunkers.