It seems, that org.gradle.plugins.ide.idea.model.ModuleDependency#exported do not honor transitivity settings. See original user report at http://youtrack.jetbrains.com/issue/IDEA-125971
I haven’t tried the test case attached to the bug report yet but according to the description it sounds like something what deserves a fix in Gradle.
In our company eGym.de we are using IDEA 13 Ultimate and we are trying to migrate our multi project build from Maven to Gradle. Everything works on the command line, however, the issue with the transitive dependencies in IDEA (Tooling API) is a major one for us. Please increase priority.
IMHO a this is a major issue for all projects which are trying to migrate from Maven to Gradle and use IDEA as an IDE, as this is not the same behavior for Maven build in IDEA.
Perhaps the subject could be edited to clarify that this is not a generic “tooling api” issue but is specific to “idea”.