As described in Comment 23 of Issue 141758241, users should have the ability to specify which .so file or java resource to package when there are multiple ones with the same name.

An example of what this will look like in the DSL:

android {
    packagingOptions {
        jniLibs {
            pickFrom('foo.so', ':fooModule') // for sub-modules
            pickFrom('bar.so', 'groupId:artifactId:version') // for external dependencies.
        }
        resources {
            pickFrom('foo.txt', ':fooModule') // for sub-modules
            pickFrom('bar.txt', 'groupId:artifactId:version') // for external dependencies.
        }
    }
}

This functionality should be added to the Variant API as well.