I think it's a bit difficult to visualize when everything is mounted to the chassis, because the Ferrari PU looks considerably more cluttered with its tubular manifold and whatnot. But, while the intercooler is mounted above the ICE, it's within the "V" and not all that high in the grand scheme of things. And you also have to consider that the Mercedes ICE is
heavily reinforced, especially at the top, to maintain absolute rigidity in order for the 125,000RPM shaft that connects the turbine to the compressor to spin freely. Its turbine is also mounted quite higher than the Ferrari turbine.
Basically, the Ferrari intercooler occupies the same space as Mercedes' compressor/MGU-H/turbine assembly.
Mercedes
Ferrari
I think both could have done better if the regulations allowed it, but that's racing, so everything is relative, yanno?
EDIT: I think you're right about the cooling systems and the PU, though. The intercooler is included in the PU as far as what manufacturers are required to package for customer teams, but they're defined within different sections of the technical regulations.