Still testing this. I have a multi-store setup with a custom package. When I set exceptions on one of my stores for the iPhone theme I get the footer data from my default theme.
Here is the layout of my packages and themes and how they are setup in the admin > config section.
Custom Package has 3 different themes: Default Theme, Theme1, Theme2 and iPhone Theme.
Custom Package is set as the Default Config package and uses the Default Theme.
When I put an Exception for the iPhone Theme on Store 1 > Theme > Default, the iPhone footer template pulls the Default Theme’s footer template.
When I put an Exception on Default Config on Theme > Default, the iPhone footer pulls its footer template like it should.
So it appears that Magento has a few glitches when using exceptions in a multi-store configuration.
Let me know if you have similar findings.