Hi Fabio.
First, I would be surprised if your S1 had a Maple neck with no other wood laminates; that would be rare. And, unlike the Signature Standard, I would have to say the same thing about a Signature Deluxe. I would imagine the Deluxe has Purpleheart laminates, and if so, they would contribute significantly to the tone. Same with the S1, depending on the year, it may have Purpleheart or other laminates as well as the Maple.
But you are right to think that the neck woods contribute significantly to the tone of a neck through bass, and the Brown Bass is going to sound different. Also the body core and top and back laminates also contribute to the tone; and there again the Brown Bass's overall combination of woods give it its unique tone.