Child themes for custom themes or similar ability plugin?

Most of our users will be using the same default theme. Some users will need a custom footer or header or CSS. The problem with just duplicating the default theme, customizing it and uploading it as a renamed theme is that if the default theme has any changes or updates, we then not only have to update the default theme, but any secondary customized themes that we may have built....

Ideally we would like to be able to make customizations for users that act in a child theme fashion. We might somehow upload a customized footer or code, but the client's theme still uses the core default theme for everything else.... this way if we upgrade the core theme, even a user with a customized footer or header receives the update.

Was looking at the userthemes plugin and not sure I fully understand how it works (maybe I don't), but it appears you actually do make a full copy of any theme you want to customize, customize it and them simply upload it to a new home in blog.dir .... which means when the default theme is updated, we would still need apply the updates to any customized themes living in blog.dir ... which apart from enabling code editing capability (not interested in this) doesn't seem to me to be any different than simply uploading customized themes with new names to the default MU themes folder.... then simply going to blogs > edit > and enabling the specific custom theme for the specific blog you are customizing ....

Anyone have any feedback on how we might accomplish this? Am I misunderstanding how the userthemes plugin works? Any feedback appreciated!