Yes, they sell many identical items, but that doesn't make them the same market. Just like many of the same things can be bought in the US and Canada, that doesn't mean that the US and Canada are within the same market.
This isn't like Walmart and Target, or Home Depot and Lowes, or Walgreen and CVS, where I can easily look for a product in one, then cross the street and look for a product in the other, then buy from whichever sounds like a better deal to me.
Android phones and the iPhone are within the same market, so the iPhone itself is not a monopoly. The iOS App Store, however, is.
If someone wanted to sway my opinion on this, I think a good angle to look at would be comparing the iOS App Store to a concession stand... except no, that still doesn't work. I was going to argue that once I decide to see a movie in one theater, I'm going to use their concession stand, but that's nonsense - I, like most people, smuggle most of my candy in from other stores in the area. Something which can't be done on iOS - I can't smuggle an Android app onto my iOS device.