"Umm... the main advantage of special shoes is that you can't slip off the bike! "
Yeah, the article does mention this. Also mentions sprinting and short, steep climbs.
I get the impression this chap Grant Petersen is trying to counter the increasing domination of proprietary racing technologies in areas of cycling that, frankly, don't really need to use them.
So it's a different "velosophy" as he would put it.
"*not* using special shoes is more efficient and less likely to lead to repetitive strain."
Well even on this forum we've had tales of "hot spots", sore knees caused by poorly adjusted cleats, etc. So I reckon there must be something in it: locking your feet into one parallel position for long periods of time could cause repetitive strain injury. I'm less taken by the "efficiency" argument, but I'm also sceptical about the largely engineering based approach that sees the human body as simply a mechanical piston.
Again if we look at Petersen's world view, it comes down to a dichotomy between "racing" and what he calls "unracing", ie. cycling that's not competitive sport. He's making the point that, unless engaged in the former (eg. as you said your livelihood depends on it), you really don't need clipless pedals, which I think is fair enough.