Header (CSS) and footer (JS) are not being added to layouts as expected

[sheerid]

The following layout update XML intends to add some CSS to the header and some Javascript to the footer. It appears that due to the theme configurations of various Magento installs, these blocks do not get appended as expected. The result causes various symptoms, including forms not being dynamically shown and SheerID UI components (most notably the organization combo box) not being rendered.

https://github.com/sheerid/sheerid-magento/blob/master/app/design/frontend/base/default/layout/verify.xml