So, after a lot of thought and careful reflection, I have determined that I and others who have criticized Bethesda's interpretation of Fallout lore are wrong, and should probably apologize to the people who have defended the game.
So, to those I have upset or crossed blades with: I am sorry.
The reason I (and others) have been wrong is an assumption based on Bethesda's chosen naming scheme: Fallout 3 and Fallout4. This choice led me to believe that Bethesda was intending to pick up where Fallout 1&2 left off, when in reality their intent (very poorly explained in or out of game) has been to spin their own separate and distinct timeline.
The division point is the same as Fallout Tactics, in the Black Isle universe, the Brotherhood of Steel never tried to become a major force, they were content to use their knowledge to help the fledgling NCR (only to later be betrayed, but that is not important here.) In the Tactics universe the BoS built their airships, and headed out to destroy the remnants of the Master's Army, and in the process unified the Midwest under the BoS banner. In the Bethesda universe the airships happened, and maybe the unification happened (insufficient data, the intolerance for non-humans leads me to believe that the unification did not occur), then they spread east eventually arriving in the Capital Wasteland.
I am not going to forgive certain distortions of established lore, but overall this realization has helped me come to terms with Bethesda's vision for Fallout.