There is no reason why the 400F5.6, in an updated version, can't have the same IQ as the 400F2.8. It's that full stop faster that you pay so much for.
For example, the 24-70 F4 and the F2.8 are similar in IQ, but twice as much for a half stop.....
The 70-200 F4IS and F2.8IS are similar in IQ, but twice as much for a half stop....
Not to sound too pedantic, but the difference between f/5.6 and f/2.8 is two stops, not one. (Which only further reinforces your point.)
That's not pedantic. It needed to be said, or the author might have continued to make this mistake.
There's also a reason an f/5.6 lens can't be as sharp as a really good f/2.8 lens - diffraction.
Diffraction does not affect FF until around f/11. Diffraction doesn't even affect APS-C until f/8 . An f/5.6 lens can be every bit as sharp, or sharper than a f/2.8 lens. Large aperture does not necessarily mean sharper images, even stopped down. Just look at the Canon 50 f/1.2L, which is not as sharp as the 50 f/1.4 at comparable apertures.