Testing the behaviour with AdminStudio 5.0, I performed these steps:
1) generated new Merge Module project (*.ism) in Developer
2) added a Component (there are no Features in a MM), built it and resolved any errors
3) saved the project as a template (*.ist)
4) took a Repackager project which was ready to be built in to a Developer project and selected
....a) a Merge Module template
....b) a Developer template
From the Merge Module template, I received the error: 'An unknown error occurred.' Using a Developer template, it built the project without error.
In the Repackager, the Repackaged Output view, you can select to 'Use a customized template.'
The problem is probably in the fact that the Merge Module projects do not have features.