Hi Paul, I thought the same thing when I got my S-2, WOW no tone controls. But have found that the low pass filters and continuous Q controls allow me to shape the tone any way I want.
I agree with Adrian, use your rig for the TONE controls, if needed.
As for the extra lam of Ebony, I'm no expert but can say that I am having a bass built that has 2 extra lams of Ebony.
Looks to me that you did your homework, knew what YOU wanted and ordered it that way.
Mike is right make it your dream. If you want to add tone controls go ffor it.
This is going to be a real cool bass.
Peace Olie