I dont think the article depicts real life shooting. Test charts are a flat surface and are not done at varying distances. when a lens is shot wide open, things like field curvature or tilted elements may not be factored into that shot. What matters more is if in focus shots are sharp or not.
You can tell if it's not sharp if you have enough experience with whatever lens you use. I've used multiple copies of the 70-200, havent met a soft one. As long as you land AF, with good shutter speeds, you're golden. If your settings are iffy, all the test charts in the world wont save the photo.
While I agree with all of your post, I guess my audiophile background keeps telling me..... the source is the most important. Without a good foundation (turntable, CD player, lens, etc.) everything further down the chain will be compromised.
I'm not as worried about my new 70-200 f/2.8 ll as I'm projecting. I already determined that it focuses very quickly and that shots at both 70 and 200mm are sharp enough to satisfy me. I'm not one of those people who expects every pixel to be sharp while shooting at f/2.8. 
Heres a full size and crop from that same shoot. The fireplace is my wife's pride and joy! These were shot with my 16-35 f/4L at 16mm.

) in the avatar, yet your recently posted shots show much reduced evidence of same!


