This is an old legacy issue in the theme before we had tons of color options and separated them.
Those specific defaults are handled in the generate_option_defaults
filter: https://github.com/tomusborne/generatepress/blob/3.1.3/inc/defaults.php#L54-L58
So it would be this:
add_filter( 'generate_option_defaults', function( $defaults ) {
$defaults['background_color'] = 'var(--base)';
$defaults['text_color'] = 'var(--grey-1)';
$defaults['link_color'] = 'var(--grey-1)';
$defaults['link_color_hover'] = 'grey-3';
$defaults['link_color_visited'] = 'var(--grey-1)';
return $defaults;
} );
The rest of the color defaults are handled in the generate_color_option_defaults
filter: https://github.com/tomusborne/generatepress/blob/3.1.3/inc/defaults.php#L121
Let me know if that helps or not ๐