To set up the default colors for the color picker of custom type fields, simply add a JavaScript snippet to override the default configuration.
In your functions.php file, add the following code, and configure the palette as you wish:
add_action( 'admin_footer', 'backgroundColor_hook' );
function backgroundColor_hook( $hook_suffix )
{
?>
<script type="text/javascript">
jQuery( document ).ready(function() {
jQuery('.js-types-colorpicker').each(function(){
jQuery(this).wpColorPicker({
palettes: ['#d21268','#146c52','#82b600','#00949b','#010080','#001c4b']
});
});
});
</script>
<?php
}