These Xcode components, installed later through the app, might touch delicate areas of the system which the MAS installer has no access to. Why wouldn't Apple just put everything that is needed on the MAS installer? Probably an issue with permissions MAS applications aren't supposed to ask for your password to install. I suppose Apple distributes its MAS Xcode with users with stable internet connections and single-install in mind, while the website version for users who might want to deploy it to several machines, in which case it would be a drag to have to download any extra-crucial elements that don't come with the installer package.
It wouldn't surprise me if it were, as this framework seems to be needed before Xcode can start. I suppose this must come bundled with Xcode from the website. I have Xcode from the App Store the first time I opened it it asked to download the Mobile Device Framework to proceed. The size difference might be due to additional files Xcode from the App Store doesn't download by default, that Xcode from the site might have.
