No, you do NOT clearly see two flags. What you see is one flag and then those buildings in the background. Your "second flag" is not the same shape as the first flag, and your "tip of the third flag" is not shaped like the tip of either of the first two shapes.
The reference photo they showed for comparison, in which you can't see those buildings in the background, was taken from a different angle and taken at a time when the vegetation is better filled in and more lush. I conveniently provided a bird's-eye view image from MSN's map service, which allows you to look at it from the north, east, south and west. The view I posted is looking at it from the east, while both Obama's picture and the stock photo are generally south.
Let me see if I can make it more clear with images.
1. The flag.
2. Building in the background.
3. Smaller building in the background.
4. Shadow of the flagpole. Notice you don't see a second flagpole.
I've attached both the blow-up of the Obama picture (further blown up another 300 percent) as well as the MSN bird's-eye view, with the same places outlined with the same numbers.
If this doesn't convince you, then I don't know what to tell you other than this stupid shit is making the rest of the GOP look bad and that's the last thing the GOP needs right now.
I mean, really, they needlessly spend hundreds of thousands of dollars, needlessly spook a bunch of New Yorkers, totally flub up the whole situation, and yet a photoshop job no one actually did, nor would there be any reason to, is getting this much attention.