If you buy it here, you do not get it from the App Store, and vice versa (though you could still download a trial version here). Omni products have a built-in software updater, which to my mind nullifies one of the main advantages the App Store provides to the purchaser.
There is discussion of some of the pros and cons in this thread:
http://forums.omnigroup.com/showthread.php?t=19616
I'm of the opinion that buying directly from Omni is better for anyone who intends to be a serious user.