Is possible Unity IoC of Prism get all the common interfaces from the modules?

If your implementations of IModule take a container as ctor parameter you can register each module's implementation of IFactory in the module's Initialize()method.

public class MyModule : IModule
{
  private readonly IUnityContainer container;
  public MyModule(IUnityContainer container)
  {
    this.container = container;
  }
  public void Initialize()
  {
    this.container.Register<IFactory, MyFactory>("MyFactory");
  }
}

public class Shell
{
  public Shell(IFactory[] factories)
  {
    // work with factories
  }
}

I consider the modules to be part of the infrastructure and not the application itself so I find it acceptable to reference the container inside the modules. Nevertheless: If you ever want to move away from Unity you would have to change that code.

If you don't want to use Modules in that way you can have a look at the TecX project. It contains an enhanced configuration engine for Unity that allows you to modularize your container configuration per assembly and collect all that information from a bootstrapper.