There aren't that many differences between the two so let's go through them one by one.

Prices, Discounts and More:

With the version sold through the Online Store I can offer discount prices for upgrades, opportunity of trial versions before the purchase, opportunity to try beta versions getting to try new features before everyone else, discounts for students and teachers, volume purchases and more.


Notice that the two versions of the Software are not interchangeable. If you bought the software from the Mac AppStore you won't get any perks limited to the version of the Online Store and vice versa if you bought from the Online Store you won't get autoupdates from the Mac AppStore (even though you will still get automatic updates, you'll need to turn them on from Preferences -> Advanced -> Updates. You may notice that if you install the app from the Online Store the Mac AppStore will mark it as "Installed", this only means that the app is already installed on your system, it doesn't mean that the app was purchased from the Mac AppStore, nor that it will get automatic updates from it. The Online Store version gets also updated quickly since it doesn't need to get through Apple Reviewal Process with every update (7 to 14 days quicker).


The other difference is Sandboxing, which is required to be on the Mac AppStore for this reason the Mac AppStore version doesn't support automatic restart of the application and automatic *starts the app on login*.