I have preached about the power of Sales Set functionality at CWG Conferences. One of the best features of Sales Sets is the ability for a user to make ad hoc, manual changes to the configurable sale BOM structure.
I saw a post on the CWG Forum tonight where a user made these settings but was still unable to make manual changes to the sales BOM. If your configuration profile is sales set and you have allowed manual changes, you can manually change the sales BOM items BUT unfortunately you must make changes in the Result screen of configuration, not in the sales order itself. I don't know of any users that find this to be intuitive (but it is what it is). Advanced users can leverage this feature to make design-to-order changes in the sales structure similar to the way that order BOMs allow design-to-order changes in the manufacturing structure.
Note that once an item is manually changed or deleted, no automatic updates will be made to that item if the configuration is later changed. Be advised that manual sales set changes can behave in a quirky manner if you are manually changing items that were specialized from a class node.