you could write a plugin / class to extend the plugin like so :

example:
create a directory called ‘wppizza-custom’ in your plugins directory.
add a file in said directory called ‘wppizza-custom.php’.
add the following code to that file:

<?php
/*
Plugin Name: WPPizza - Custom Vars
Description:  WPPizza - Custom Vars
Author: ollybach
Plugin URI: http://www.wp-pizza.com
Author URI: http://www.wp-pizza.com
Version: 0.1
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
if ( ! defined( 'ABSPATH' ) ) exit; // Exit if accessed directly
add_action( 'plugins_loaded', 'wppizza_extend_custom_vars');
function wppizza_extend_custom_vars(){
if (!class_exists( 'WPPIZZA' )) {return;}
class WPPIZZA_EXTEND_CUSTOM_VARS extends WPPIZZA{
/************************************************************
*
*	[construct]
*
*************************************************************/
function __construct() {
parent::__construct();
/**set/customise  vars**/
$this->wppizza_set_custom_vars();
}		
function wppizza_set_custom_vars(){
/**
overwrite whatever needs overwriting
to see all vars just do a
print_r($this->pluginOptions)
**/
$this->pluginOptions['order']['order_pickup']=1;/*enable custom pickup for example even if it's not enabled in order settings*/
}
}
}
?>