Interesting and well thought out article Thierry.
z-index has always been a pain to manage (especially in the early days when IE didn’t understand the auto value). It also just became harder now that webkit pulls fixed positioned elements out of their current context (contrary to the specs).
To me it would have made more sense for z-index to be simpler and a higher or lower z-index wins out as required. Atomic stacking contexts often fail because you may want a graphical element of your design overlapping a number of columns yet you will still want a flyout or popup being on top of this no matter where it is and adjusting the z-index of the parent dynamically breaks this layout and indeed things like shadows on the elements/columns will be lost while the dynamic effect takes place.