I don't think this is the intended way either.
When you download beta 3, Xcode is downloaded as a zip and iOS is downloaded as a dmg
The intention seems to be that when you run Xcode, it should use the iOS dmg file. however, it downloads the iOS component again.
Also, the Xcode zip should be unzipped to into /Application rather than /Downloads
The steps needed are
Download Xcode an iOS
Move the Xcode zip to \Applications
Unarchive Xcode by opening it
The rest is a mystery
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FYI see FB12453767