My guess is that if you wanted to install more powerful woofers (as opposed to a 'subwoofer'), what you could do is take the existing signal that goes to the woofers in the rear doors and re-route that signal to a more powerful woofer that you could locate elsewhere in the car. You likely would not notice the loss of the two rear door woofers, especially if you place your more powerful woofer in the back of the car.
The difficult part is going to be determining exactly where to put the more powerful woofer... there really are not many choices available. You can't put anything on the underside of the hatshelf because all the space under the hatshelf is occupied by controllers and electronics - that area is the 'server room' of the Phaeton. You can't put anything behind the rear seat backrest because there is a steel wall right behind the backrest. You can put anything under any of the seats because all the space under every seat is taken up with seat controller components.
About all you could do (best I can figure out) would be to replace the two rear door woofers with more powerful aftermarket woofers, and of course a secondary (downstream) amplifier to drive those more powerful replacement woofers. That would require a bit of fooling around and custom installation work. Or, I suppose you could put a single woofer in the place that the ski-bag goes now, then put a fabric screen over it. That would require that you leave the rear seat middle armrest open (or, that you load a drum solo into the CD player to blow the rear seat middle armrest forward into the down position).