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Not much difference. The "advantage" to the package allows you to book transport to hotel as well as get regular dining plan- but both aren't good values.
One of the major differences is the fees that you pay if you make any changes to your package. With room and tickets only, you can make changes and even cancel you room within 6 days of arriving.
There’s really no good reason to book a package if you are staying on site unless it is during the celebration of Harry Potter. If you want to stay offsite and still get early entry, booking a package is the only way to do it.