If it's the same model then there would be no difference.
If you feel comfortable getting to know your machine without benefit of a class that a local dealer would provide, and the price is far better (including shipping) than a dealer can provide ... then go for it.
You might want to give your dealer a call to see if they would honor a Janome warranty if you did not purchase your machine through them.
If your dealer will not honor the Janome warranty then I would make the 60+ mile trip (to me that's not far at all) to the dealer to get the machine and get a training class on the same day. This way you are covered by that dealer should you ever need service.
While your at it ... explain to the dealer why you are asking if they would honor the Janome warranty and tell them the price you are looking at online. They might be able to match it.