Oh, and just to be clear, it's actually not a server config that's returning the theme when accessing / (index.php), it's an actual file set up under the root at index.php that does this:
define('WP_USE_THEMES', true);
require('./blog/wp-blog-header.php');
Whereas the version under /blog looks like this:
define('WP_USE_THEMES', true);
require('./wp-blog-header.php');
So I'm trying to figure out how to get WP-supercache to flush the root index.php page even though it sits above the /blog subdirectory.