The advantage is that you eliminate the weight of the pylon. The downside is that if the upper engine has a fuel (or other fluid) leak, it drains down into the lower engine so both can burn evenly... From a practical stand point, the stacked engine design makes maintenance very difficult because the upper engine is hard to reach and worse to change-out (must use a crane). When both engines hang side-by-side on a pylon, they are equal heights from the ground and are closer to it making maintenance easier and both will use the same lifting device for change-out. No special tools required unlike those needed for the upper engine in this case (the Sperrin design is even worse in this regard because the upper engine is not only high but over the wing as well).
Phil