I think the situation is that stores can have small inventory levels of an item and below a certain threshold (I've read the number is five, for watches) inventory doesn't show up online. This avoids disappointments due to inventory mistakes (happens, even at Apple) and also gives the store a cushion for in-store replacement of items returned because they aren't working. I don't remember personally running into this with watches, but I have had it happen several times with MacBooks.
Another thing to remember is that Edition watches are limited to select stores. I live in Massachusetts and there is only one store in the Commonwealth that sells them (the flagship store on Boylston Street in Boston).