If Microsoft wants to start doing that in their app store, I don't see why they couldn't. But they'd be competing with all the other app stores available for buying PC software (as well as physical stores selling physical media).
But Microsoft doesn't make hardware that's the only target for their desktop OS, so they don't have the market lock-in Apple does, nor could they claim the app store and the hardware they don't make are part of the same product for PCs running Windows.
In contrast? They already do this for the XBox Live store, where they are the sole online distribution channel for software running on the console they manufacture.
But Microsoft doesn't make hardware that's the only target for their desktop OS, so they don't have the market lock-in Apple does, nor could they claim the app store and the hardware they don't make are part of the same product for PCs running Windows.
In contrast? They already do this for the XBox Live store, where they are the sole online distribution channel for software running on the console they manufacture.