I don't know Sak's rules exactly
shaggy, but in European dept stores the rules of the dept store tend take precedence.
It's true both have different rules eg Gucci stores do not offer a full refund (only an exchange before 14 days) but large dept stores might do - but the waranty is part of Gucci's guarantee of quality as far as I know and should honour their commitments wherever you bought so long as it is Gucci-made.
I would Saks AND Gucci for details of the implications of purchasing via the dept store rather than from Gucci directly.
I know you didn't ask about returns but I will add: shop where ever you are happy and comfortable just be warned that it's difficult to mix the two, if you buy at a Gucci store you cannot return the items for an exchange to a dept store and vice versa.
Don't forget that you can call your usual Gucci store and give them the model no of the bag you like thay can order it in so long as it's current season's stock