It turns out that the major contributor to charge heating is the heat transferred from the turbine to the impeller.
The current Mercedes F1 engine separates the turbine from the impeller by a long ceramic shaft. This eliminates heat transfer, and they manage without an intercooler altogether. This in turn eliminates a huge amount of air pipe (helped by the turbo being at the back of the engine and the impeller at the front) simplifying the whole installation and gaining aerodynamic advantage as a result.