When the Mac App Store launches, it apparently scans your computer for a list of those bundle IDs, which it likely pulls from a centralized OS X system called Launch Services. (You can pull up the list yourself with a little --scroll down to the comments for the most recent version of the command).

If the store detects an application installed on your system where both the bundle ID and the app's version match the information associated with the app for sale on the store, that app gets marked as Installed. Those are the apps that where the developer chose to use the same bundle ID for the version in the Mac App Store as the one that it sold elsewhere. (Note that those apps do not show up in the list of Purchases that you can access in the Mac App Store.)

Red Sweater Software founder Daniel Jalkut told me via e-mail there are pros and cons to each approach. The problem in the first case, he says, is that users may believe that--because the app is already listed as Installed in the Mac App Store--they'll be able to get updates through the store, write reviews, and so on, even though that isn't the case.

However, apps that use a different bundle ID for their Mac App Store version present separate challenges. In that case, as Jalkut points out, the store will still show you the option to buy applications that you've already purchased elsewhere, potentially leading to unintended double-purchases--a risk exacerbated by the fact that the App Store has trained most users that they can re-download an app for free and because the Mac App Store doesn't currently ask for confirmation before a purchase.

Seeing double