I wanted to standardize the fonts for all the Microsoft Office Outlook 2003 clients in my domain, so I configured the fonts on one machine and exported the HKEY_CURRENT_USER\Software\Microsoft\Office\11.0\Common\MailSettings registry subkey to get the right value to deploy by using either a script or the Custom Maintenance Wizard. That worked, but the subkey doesn't include the configured setting for Automatically display Rich Text in draft font when using high contrast. Does a different registry subkey control that setting?

Your hunch about a different registry subkey is exactly right! Outlook stores the font settings in Office\11.0\Common\Mail Settings because both Outlook and Microsoft Word (if Word is the email editor) need to use them. The registry value you're looking for is in the HKEY_CURRENT _USER\Software\Microsoft\Office\11.0\Outlook\Options\Mail subkey, in a DWORD value named AutoDraftIn HighContrast. A value of 0 turns the setting to display Rich Text off, and 1 turns it on.