When the Setup/ diplomacy charts are finished and released in Highpes (this upcoming week) they will be the same size as the box tops. My intension was actually not to have them pasted over the existing box-top, but rather create a double sided Setups Unit Stat/ Diplomatic + Nation Rule chart which would fit snugly inside each nations box.
if you decide to paste the setup on the outside of the box. you should consider putting the diplomacy card side on the inside of the lid. Note: there are enough boxes in AAE40 + AAP40 boxes to give each power its own box.