Some people have it show up as installed, some don't. At this point, no one's 100% sure as to the reason (seems to be tied to bundle ID's for the most part, but even that's not a sure shot right now).
The important, take-away point, however, is that the only difference is that if it shows up as purchased you can't easily (accidentally) purchase it again. You won't get updates through the Mac App Store, you won't be able to re-download it from there, etc. You got it from another source, it doesn't gain any of the benefits of the Mac App Store magically just from already being on the computer.
jW