There's actually more than enough room there. Notice the AudioPipe distribution block (used for the ground back to the battery) in the first picture. That thing sticks out 1-1/2" and doesn't hit the seat. These ID12's have a 13.5mm(0.53") one-way Xmax. So even at full pop, they have at least 1/2" of clearance - even at the top where it's the tightest.
You bring up a terrific point though, as this was a critical consideration when designing the box. I could have brought the face of the box forward if it weren't for the way the rear seat-backs hinge. As you lay them down, the leading edge gets closer to the back wall. It is very tight when the seats are laid down, and that's the only reason I had to remove the plastic covers from the seats. With the seats upright and locked, the driver still has plenty of clearance - even with the plastic panels installed. But the plastic hits the driver surround when the seat is laid down.
You will also notice that I have spaced-out the seat lock tabs with 1" thick UHMW and longer bolts. This also serves to improve excursion clearance, but is not the reason for the spacers. I needed the spacers to get the proper box volume while allowing for that clearance. Again, the clearance issue is with the lower section of the box when the seat backs are folded down. That is the limiting factor for depth at the bottom. The spacers allow the top of the box to be deeper - providing necessary box volume that you can't get anywhere else. Building out, into the side pockets and up in front of the upper support beam don't provide any volume once you factor-in the 3/4" MDF board thickness, so there's no help there. If you’re going to get it, you have to get it from the upper section of the box.
Great question!