We just had the experience where someone added a new module to the project. Gradle’s IDEA plugin did create the new .iml file, but nothing actually linked it into the project. We ended up separately hand-editing .idea/modules.xml and manually committing it.
It seems like this could be easier. For instance, since Gradle is the one creating the .iml files (we don’t have them checked in anymore), maybe it should be updating modules.xml itself.