What if you did this. Since you already have the box for the subs just keep it centered. Then build a trim piece that goes OVER the sub box and fits to the sides of the trunk same as the install you posted. Since your subs are not flush mounted currently adding the piece of MDF on top of them would still look fine. This would save you from rebuilding the new enclosures. Plus with seperate enclosures like shown above you would have to make sure they are both EXACTLY the same volume or your will experience some cancelation.

As for the amp you could then do a hinged false floor for the amp so you still have access to the tire. Or you could try and build it to one of the sides of the trunk. Just make a flush fitting piece for the side, cut it out mount the amp behind it, maybe add some plexi and you would be good to go. If you have components in your car you could do the same with the crossovers on the other side so it looks more balenced.

Just an idea.