You are not missing anything. The MinimumOSVersion Info.plist key is system-set and even if you set it in Info.plist yourself, Xcode will override it at build time.
Currently, you do not have control over the minimum OS version because you do not have any control over the Xcode settings that AppBuilder is using for building your app. Is there any particular reason why you need to change the iOS 5.0 value and what is the minimum OS version that you would like to target?
In addition, if you want to be able to have control over the minimum OS version, you can submit a feature request in our feedback portal
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