Alan,
While I would agree with you that the "branding" concept makes good sense if you are planning on complex graphic overlays, getting the base theme color as is available on the Windows Phone using a static theme brush provided by the OS is a better choice for base color themes in your app. The user has chosen that color because they find it pleasing to the eye. Even more important, certain users may be color blind to one or more colors and have chosen the best option to enhance readability and accessibility.
Having access to the standard color scheme allows you to stay within the light/dark theme and meet the accessibility standards required by many corporations for all programs for those that are visually impaired.
The SDK is in it's infancy and it is possible that this important feature has been left out of the current implementation because it was not ready for the release of the SDK (colors might not have been finalized or compatibility of the theme on certain devices was still being developed).
It isn't too difficult to derive the theme color from an existing theme brush that is given to you such as ProgressBarForegroundThemeBrush by adding/subtracting values to get the current theme color.
My suggestion would be to adhere to the theme styles as best as possible to ensure your application will remain current regardless of changes to the operating system.
I have been a Windows Phone programmer since May 2010.