App Store wouldn't recognize my Logic Pro X
Logic Pro X is only available on the Mac App Store and the Logic Pro X bundle will contain a MASReceipt that tells the Mac App Store who the app is registered to.

This means the Mac App Store won't claim knowledge of the app unless you are signed in with the Apple ID that you used to purchase it. As you say you didn't purchase it from the Mac App Store, it won't be assigned to your Apple ID and the Mac App Store won't update it for you as it sees it immediately as pirated software.

Aperture is available elsewhere on physical media. This means that there won't be a Mac App Store receipt assigned to the app and the app can be assigned to an Apple ID.

This means that the Mac App Store will assign your Aperture that was purchased outside of the Mac App Store to the currently logged in Apple ID. This is the same for the retail version of iWork which can be purchased elsewhere and the Mac App Store will 'accept' it (like iLife).



You can read more about this problem when it occurred on this blog post by The Verge:


The Mac App Store is upgrading illegal and trial software for free