Similar to bug 107731, the colors in Tools > Options > LibreOffice > Application Colors are no longer available in the new default color palette. Similar colors from the new standard palette should be chosen so that the colors are selected in the color picker widget.
Colors defined at the application level shouldnt be limited to a document-level color palette, which is how it was before the new palette was introduced. e.g. Text boundaries is set to c0c0c0 and the old palette only had b2b2b2 and cccccc.
Alright, and how could a user restore the default color of one item when it's not available in the palette?
There is an 'automatic' button located at the top of the widget. If you dont see the button, then maybe the fix in bug 107981 solved the issue there also.