Hello Ioannis -- thanks for your kind words.
A quick reaction to answer your questions.
1) The 'puzzle pieces' are constructed such that putting them together enforces a XOR relationship between the blue disks and the (yellow) voids. You can indeed build the same pattern using the puzzle pieces you proposed, but these can also fit together in many ways that violate the XOR relationship.
2) Not sure what you mean by 6 bits being only needed for the second configuration in figure 2. Can you elaborate please?
3) The superposition you can imagine as resulting from putting the left and middle configuration of figure 2 on top of each other. There where two blue disks are stacked on top of each other, you remove both disks. In all other circumstances (0 or 1 disks on top of each other) you leave the situation as is. The configuration that results is the one shown on the right-hand side of figure 2.
Regards,
Johannes