The current IntelliJ gradle plug in places (by default) the class files generated by intellij and by gradle in the same place. However compiling in IntelliJ also copies resources to the classes directory. If you now build a jar file with gradle, all the resources will be duplicated in the jar file. Gradle is copying them from the original location as well collecting the copies added by IntelliJ to the classes directory tree.
Some of my software objects strenuously to duplicated entries in jar files. In any case it is a waste of space.
So while using the same output location is a good idea (in my opinion), it has an unwanted side effect.
Using IntelliJ 13.1.4.