Many times packagers use merge modules for applications to prevent conflicts when uninstalling that application later on. Here's a "best practice" to keep in mind when using merge modules.
There are drawbacks to merge modules, such as if a patch comes out for something in that module. You would then have to create a patch for each application you have.
You may find that it is better to ban merge modules altogether. Instead create a MSI for each of your merge modules and then make them a pre-requisite for the application that requires it.
The benefit of this is that when a patch comes out for whatever is in the merge module you only have to deploy one patch instead of a patch for each module.