After completing the third row install in a V70R with the factory sub, the simple answer is no.
In a car with no rear hatch accessories, there is a storage tray and tire jack is stored inside the spare tire, around a plastic false floor pedestal.
With a sub, the storage tray is removed and the jack is stored in a foam mold above the spare tire since the sub itself rests inside the spare tire.
The third row also removes the storage tray but the jack stays inside the spare tire. However the support pedestal is much shorter because the third row's carpeted wood false floor dips into the spare tire so the rear passengers have a bit more room for their feet.
The only way you could keep the factory sub functionality would be to remove the factory amp from the original enclosure, extend its wires to a custom enclosure that housed a small 8" slim sub that would displace the jack and pedestal.