You can also use additional TOCs in your master project in order to create alternative outputs using different combinations of modules and native topics from the master project. You just need to create an additional TOC and insert references to the child modules there.
See Multiple TOCs for details on how to create and manage additional TOCs.
"Copying" modules is not possible because they are really only references to entire help projects. Also, you cannot copy modules within the same project because duplicate module references are forbidden. If you want to insert the same module in a second project you must do this directly.
Similarly, you cannot insert a second copy of a module entry within the same project. This is not allowed because it would cause irreconcilable conflicts because of the duplicate topic IDs and context numbers it would create.
Circular module references:
This is something you need to be aware of yourself because Help+Manual cannot prevent it automatically and it can cause serious errors. A circular reference is a module that contains another module that then contains the first module. For example, suppose Project A contains Project B as a module. If you then open Project B on its own and try to insert Project A as a module the results in your output can be both unpredictable and unpleasant. Don't do it.
You can use conditional output include options on entire modules in the same way as you can on individual topics. To do this select the main module entry in the TOC and then select Project > Change > Include in Builds to select the include options for the module. You can also access the include options by right-clicking on the main module entry in the TOC. See Modular projects include options for full details.
Even when the TOC of the your child project is visible in the master TOC you cannot see all the child's Topic Files and Configuration settings directly. Only the topics with TOC entries are actually displayed in the master TOC. You can access topic files without TOC entries and the child's configuration settings in the Merged Projects section in the Project Explorer:
This section is located right at the bottom of the Configuration section. Note that like the TOC, the files and settings of merged projects are only shown for projects inserted in publish-time merging mode. Runtime-merged projects are just placeholders and are not really part of your project, they must be opened and edited separately.