You are right Denny. I'm pulling both sides of the rope here. Wort stratification is something that doesn't make a lot of sense to me and the Mr. Wizard article seems to support your point. I felt like I observed wort stratification early in my switch to 10 gallons and for that reason along with a few others implemented a system of running off into two carboys simultaneously. That became part of my method and I haven't really thought about it for a long time.
One thought as I write this... temperature affects a liquids ability to hold sugar. Is it possible that if there is temperature stratification that this could lead to sugar stratification because it's easier for the top of the kettle that is hotter to hold more sugar then for the bottom colder portion? Therefore there would be no wort stratification at an equilabrium temp?
Think about ice-t, I can usually get all of the sugar into solution if I stir long enough but it's more work then hot-t. Perhaps if there is a limited amount of sugar in a pot the hotter wort will hold onto more of it then the colder?
If that were the case then I think the method of chilling could play a role... immersion chillers would lead to more stratification then plates and counterflows that go straight into the fermenter.
***Just brainstorming here - NONE OF THIS IS FACT