The behavior you're describing is exactly what I noticed when I made a page with a Blog module on it.  I added the module, and a whole bunch of containers appeared on the page.  It was confusing at first because they all had the same name in the container title, but I realized they were distinct units of blog functionality.

After seeing that, with your post in mind, I checked the \DesktopModules\Blog\ directory and sure enough, there's an .ascx file for every blog function and view the module supports.  I create a "Blog" page with almost every blog component on it, but I wanted Recent Posts on the front page of the site as well, so I copied the module from the Blog page via the Common Tasks pane of the control panel.  Seems to work like a charm, I have Recent Posts in two places.  (I only mention that, since it's somewhat easier than adding a new instance of the module and removing all the "sub-modules" (for lack of a better term), if the control you want already exists somewhere else.)

I also noticed that the Blog module has a funciton allowing users to choose a specific sub-module and add it to a container.  I think I might peek at the source  code and see if I can't adapt it for use with my custom data interface needs.

The fact that the included Blog module follows the same pattern you're using makes a strong case that what you figured out is the right way to achieve this sort of functionality.  I feel like I have a much clearer understanding of how to proceed now!

Thanks again!
Gabe