As far as I remember, for the past 3 years, every app put into those stores by Apple themselves received unlimited upgrades.
Everybody wanted to do paid upgrade, pressuring Apple into adding some paid upgrade feature into the store. Apple always declined, saying "do as we do, support unlimited upgrades, you'll earn enough because the market is growing".
Some devs did paid upgrades by creating a new app with a new name, creating some issues along the way (people that just bought the old version a day ago have no upgrade path etc.) Not idea.
People guessed that Apple would add some "paid upgrade" feature once they needed it themselves.
Now Apple decided for the first time to create a paid upgrade, and apparently they - just created a new app...
Apple could have done better here.
AppShopper also automatically started tracking them as 2 items: