There are two reasons that I want Aperture to be a purchased item in my App Store. First, because when the App Store was announced, we previous owners were told that if our copies of Aperture were registered with Apple, and mine is, the App Store would automatically give old owner credit for the purchase on the App Store. The same goes for any registered Apple software.
I never heard that either and am one who purchased AP2 and AP3 upgrade in succession. I eventually just purchased the MAS version so it would be a much easier and faster install / backup.
FWIW, you can also use the terminal commands to show hidden files and folders in Finder and then insert your AP3 disc in your current machines optical drive. This will allow you to copy over all the files (many of which are hidden) to a folder on your desktop.
You can then copy that folder to an external drive for backup and also use it to install (just run the installer package from inside the folder and it will install the same). I did this for a while before going to the MAS and just purchasing that version. Note - just make sure you have your serial number(s) in say a text file in the folder as well to copy and paste when needed during install. 😉