The fatal design choice was in not designing a BWB.
I see your technical point, but I disagree on other grounds. Long story short: airports already balked at adapting to the A380, although Airbus had wisely stuck with "reasonable" dimensions (a square 80 m x 80 m, no bigger).
Adapting to a BWB specifics would have been far more difficult. Airbus has to listen to airlines requirements, otherwise their big plane would not sell. And the A380 already sold much less than what they initially hoped.
Also the issues of windows and evacuations. Airports, airlines, FAA / EASA are pretty conservative for safety sake, that's why the "cylinder with wings" is still there - even if BWB is technically superior on many points.