In a manifest for a module, there is a package element, which contains components, one of which will be a module. However, DNN doesn't support having multiple module components within a single package. As a result, if an extension wants to install multiple modules, they show up as multiple packages (even if the administrator only uploaded a single zip file to install them).
One of the main benefits of allowing multiple modules in a package would be the ability to uninstall a module package easily. When a module package installs multiple modules, it can get tedious when uninstalling them all.
Alternatively, the ability to uninstall multiple modules at the same time could also be helpful. However, it's unintuitive and confusing to have the separate package and module concepts, but not really be able to separate them in a meaningful way.