Thanks for a good answer, lots of reasonable points.
I looked into three of the planes that you linked to: Vespina, the UK equivalent of Airforce One, Konrad Adenauer, the German equivalent and Cotam 001, the French. As far as I can tell, they are all just regular commercial planes with pragmatic changes to reflect their usage (eg seating layouts, private spaces, etc) and upgraded radar. They're pretty cheap in commercial jet terms.
eg. Vespina: It's a standard (new) Airbus 330 (list cost approximately $250m) with about $15m spent on refitting it for purpose. Total: $275m. It isn't fitted with ECM, EMP hardening, armor etc. It's just a convenience thing. Both the German and French retrofitted previously used commercial planes.
The next (pair of) Airforce Ones will cost the US taxpayer at least $3.9bn. Much more than 10x Vespina. Running costs are astronomical (about $100m per year)
You're probably right that there's a good case for a dedicated aircraft for senior government officials. I'm not convinced having a supposedly nuclear-hardened Boeing boondoggle one makes any sense at all. (Don't fall for the 'Boeing is losing money on this' argument, the US Government will always bail out Boeing whatever happens)