Custom module type and VCS-based project

Some of the users of my plugin are having issues creating a project from VCS (Git and SVN so far) and then using my plugin with the retrieved source files.  The issue is that my plugin has a custom module type, and the module that's created by default for the VCS-derived project is of type Java.  The workaround is to create a new module of the correct type as a peer to the default module with the same source root and then to delete the original module.  The other option is to create the project/module of the correct type for my plugin and then to checkout/fetch the source from VCS either via some other tool, e.g., CLI.  If you try to retrieve the source using IntelliJ IDEA (VCS>Checkout from Version Control) into the existing project/module, you get the error message:

"The path <path-to-project> exists.  Repository cannot be cloned to an existing directory."

Obviously not great solutions either way.

Any thoughts on how best to remove this seeming impedance mismatch between my custom language plugin's custom module type and VCS-based projects?