Another point to consider is the amortization of the non-recurring (design costs).
When a company, like Boeing or Airbus, develop a plane, they plan to sell hundreds, if not thousands of planes. So the sell price consists of profit (they do need to make money), fabrication costs (the cost to actually build a plane), and a portion of the design cost - say 1/1000th of this design cost.
Since the development may run a billion dollars (yes - they are expensive to design and test), this will add $1 million to the sell price (1 billion divided by 1 thousand)
But for AF1, they are only buying 2. Take 1 billion and divide by 2 and the sell cost has to include $500 million to cover the design cost
And before someone claims the plane already exists, every system has to be re-evaluated and possibly upgraded. The power system has to be redesigned to handle all of the special electronics. As Woody indicated, all of the wiring is probably being upgraded. And while they may not have escape pods, I'm sure there are flare dispensers, radar detectors, etc added for the protection of the aircraft. Throw in other changes and it is basically a new aircraft....