Upon taking the default sharepoint master page for MySite, making some changes, and making a wsp out of it with WSPBuilder, I come to these errors in my logs:
http://spoint/MySite/%5Fcatalogs/masterpage/MySite.master - An unexpected error has been encountered in this Web Part. Error: The control with virtual path '_controltemplates/Welcome.ascx' is not in the safe controls list for web at URL 'http://spoint/MySite'., Source: [UnsafeControlException: The control with virtual path '_controltemplates/Welcome.ascx' is not in the safe controls list for web at URL 'http://spoint/MySite' (stack trace omitted)
http://spoint/MySite/%5Fcatalogs/masterpage/MySite.master - An unexpected error has been encountered in this Web Part. Error: The control with virtual path '_controltemplates/DesignModeConsole.ascx' is not in the safe controls list for web at URL 'http://spoint/MySite'., Source: [UnsafeControlException: The control with virtual path '_controltemplates/DesignModeConsole.ascx' is not in the safe controls list for web at URL 'http://spoint/MySite' (stack trace ommited)
So, this masterpage does in fact use these OOTB controls and so I guess I need to get them safecontrolled. And I guess I want to do this via the manifest.xml. But I do not see how to make WSPBuilder do this.