I believe the only difference is whether having the extra money in your wallet causes you to sit at an angle and make all of your diagrams slightly off level :-)
For official confirmation, send an email to OmniGraffle@omnigroup.com
, but I would be very surprised to hear that there is any functional difference. There is no disclosure of such differences in the documentation in the program or on the website (unlike Pro vs. regular) and one would expect a demo to accurately reflect the product being purchased, but there is no educational demo of either program. Also, and perhaps most relevant, the Omni Group isn't a bunch of chiseling scoundrels only interested in vacuuming up every last nickel of marginal revenue by any customer-unfriendly scheme imaginable!
I offer the following advice: buy directly from Omni, not the Mac App Store, and have a look at their other offerings and see if there's anything else that you might want. Buying multiple products simultaneously gets you an increasing discount for each additional product (at least for non-educational buyers), and getting the software from Omni puts all of the money in their pocket and gets you easier access to new versions, discounted major upgrades, etc. There is a built-in software updater and the licensing terms are generous which weakens some of the main reasons for buying through th Mac App Store in my opinion.