So the duplicate Kotlin dependency is a failing of the gradle-intelli-plugin that only excludes the Kotlin dependency if there is a direct dependency on Kotlin, whereas I had a transitive one:
https://github.com/JetBrains/gradle-intellij-plugin/issues/57
That's easy enough to work around, but I still think it would be appropriate to transport the freeCompilerArgs from the build script to the Kotlin facet during the gradle import.