The module includer is a handy box which allows you to select which versions modules will be included in.
You can use the master version of your mailing to build all the possible modules that your email might need. You can then select which versions those modules will appear in using the module includer button. If your mailing has only one version you will see the option to hide the module in the Master Version instead as there are no versions to include the module in.
Once you head into these versions, you can then change the content according to what the version needs, for example, content for a specific locale.
Modules which you create in a non-master version will be available in the module includer to include in the master version, and to add to other versions. You can then add these to the master version, and other versions if you want.
You should avoid deleting modules from the master version, rather hide them from the versions you don't want them to appear in.