Yes, everything will fit in the Super CE Box, including all 20 borough boards and their associated player pieces.
We don't have a final size for the box as there are a lot of moving parts, and the decision to add the Super CE version was done after the Kickstarter began. Ideally, we'd love to have a box that works perfectly for both the regular CE game as well as the Super CE game (and we have some great ideas on how to do this), but until all the pieces, including the GameTrayz, are finalized, we won't know exactly how this will pan out.
The important thing is that regardless of which game you choose, all the components will fit in it. And not in some convoluted way that makes you force the pieces in and cram the box closed—we hate that too!