as a developer I expect that Clover will automatically configure IntelliJ IDEA compiler settings

Since IDEA12 a new external build feature has been introduced. It has also an option to perform parallel build (Settings > Compile > Build independent modules in parallel toggle), however Clover does not support parallel instrumentation (see CLOV-1284).

Clover should automatically disable the parallel build toggle whenever compilation starts (it can notify about this fact by a baloon), otherwise it will throw various runtime exceptions during compilation.