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Apple fairly routinely lets themselves be exceptions to rules for their own platform. Lion is distributed via the Mac App Store, and I'd put money on them not allowing Ubuntu or Windows to be distributed via the Mac App Store in a similar fashion[1].

1: future anti-trust cases or congressional testimonies nonwithstanding

Hypothetical rule: "Operating Systems may be distributed through the Mac App Store only if they are capable of running the Mac App Store"

They just updated xcode today. In the new update they're slightly more in compliance as it is no longer an installer that is downloaded, it's an app package. You can tell they spent some time reworking stuff to get it working correctly within those app store rules.

Xcode was not distributed through the App Store, an Installer for Xcode was distributed through the App Store.