Gradle import and nested modules

We have a large project with a hierarchy of gradle modules. When I import, I can check or uncheck "Create separate module per source set". If I check it, I get a nice hierarchy of IntelliJ modules, but each bottom-level gradle project is created as three separate modules: one for main, one for test, and one other. If I don't check it, I get a flat set of modules, whose names are somehow generated, but each gradle project is a single module, with multiple source directories.

What I would like is the hierarchy, but with each bottom-level project as a single module. How do I accomplish that?

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