Cubby is an item on punch list for any and all who don't have it according to Service Manager at Tesla, Menlo Park. They are a 2 minute retrofit. I had mine installed a week ago along with a few other punch list items (No Parcel Cover yet, grrr.). Note that it is ONLY a cubby and doesn't include a replacement for the carpeting in the center area...I thought part of the Cubby install was to include a CF or equivalent runner for the center area. Not the case. If you didn't formally add it to your punch list when you got your Model S, contact your Service Manager so they can get it for you.
I would contact your local Service Site to make sure they set one aside for you and install at your convenience.