Remove Redundant Links

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How can I change the replaced element, the title or the class name?

The current settings are chosen for compatibility.
To use other settings, you probably have to alter your theme.

You may alter the settings with a filter on rrl_settings in your functions.php.

Example:

function change_rrl_settings( $settings )
{
    $settings['class']     = 'my_own_class';
    $settings['title']     = 'Here be dragons';
    $settings['replace_a'] = 'span';

    return $settings;
}

add_filter( 'rrl_settings', 'change_rrl_settings', 10, 1 );

How can I prevent the stripping of the server prefix for links to other pages on the same site?

Same as above, set strip_server_prefix_on_all_links to FALSE:

function rrl_prevent_server_prefix( $settings )
{
    $settings['strip_server_prefix_on_all_links']     = FALSE;
    return $settings;
}

add_filter( 'rrl_settings', 'rrl_prevent_server_prefix', 10, 1);