Well, it's a Commodore 64 graphics editor, those colours are kept fixed because they fairly accurately represent the VIC-II colours, even if the palette is altered for personal taste.
It's especially important when using multi-colour mode and the 'Char' pen as the palette image then changes to indicate the "multi-colour" versions on the lower row (as seen in your image above).
ie. If you are using the app for non-C64 work then the concept of the Char pen having 8 hi-res + 8 multi-colours fails and a recoloured palette image would make no sense.
May I ask what platform you are pixelling for?