The only difference is this...
- If you buy from Apple online, you can custom configure your machine.
- If you buy from Apple online and purchase a stock configuration, or from the Apple Store and purchase a stock configuration (as they always are in store), and the computer fails or has some defect within 30 days, you can take it to any Apple Store and most managers will instantly replace it with a brand new computer. If you bought from anywhere else, you will have to go through a warranty repair.
- Apple charges a 10% restock fee, most non-Apple stores do not take any refunds at all.
- Apple Store managers have lots of power... so if anything goes wrong, or there are any issues at all... and you are nice and keep pressing, you will get much further with Apple Stores than you will with anyone else.