personally i think there is a balance.
Barefoot is not an option, Five Fingers... well, I'm familiar with Vibram and it's no Stealth

honestly, the ideal shoe for PK (in my mind) would have PK specific features(especially in the area of grip and cushion) but be comfortable enough to be your everyday shoe.
I personally would point and laugh if i saw someone wearing five-fingers walking down the street... that may just be me, but they look goofie.
yes, some shoe manufacturers do over cushion... but one of the points made in the article was about large cushion causing your heel to hit... by landing drops with correct PK form (balls of feet) in many ways you force your foot to use some of the biomechanics that this article speaks of.
what's worse is the type of cushion used... as mentioned in the article... big squishy cushion in some cases does more harm than good.