I don't know enough about engines to explain why, but the iS engine that Rotax currently sells does indeed require additional cooling capability when compared to the ULS ( the effort required to modify the original cowl exit area, and other details wouldn't have been done if it wasn't necessary).
Representatives of Rotax have confirmed this and have said that many manufacturers have had to make changes to deal with it.
The final design of the RV-12iS allows for a climb at Vy to 10000 ft on a 100 *F day with temps staying in the normal range.
Well, physics is physics. If they wanted more cooling margin then that would explain increasing airflow. Also, it seems if would perhaps be harder to get a very efficient duct shape to feed the cylinders with the extra clutter of the EFI bits on the top of the engine.