What are the advantages of buying a Mac at an Apple Store?
Aside from the service and other qualitative aspects of dealing directly with Apple, the only "advantage" of purchasing direct from the company is the up to date warranty registration. If you purchase your Apple product through a 3rd party, Apple will have on file an "estimated" purchase date based on the model's manufacturing date.

If you want to claim all of the 365 days on your warranty, you will have to send them the receipt (a scan or picture suffices) in addition to other purchase information so they can update their database to reflect the exact date of purchase.

Other than that, it makes little difference at the end of the day.