Storing Custom Post Type Data in a Custom Table

You certainly can save the data however you choose using the save_post action. Simply, place this in your functions.php file.

add_action('save_post', 'foo_save_custom_post_type');
function foo_save_custom_post_type(){
    //Use the following debug code to see what information is available to you
    /*
    echo "<pre>";
    print_r($_REQUEST);
    echo "</pre>";
    exit;
    */

    if('custom_post_type' === $_REQUEST['post_type']){
        //Do your custom table bidding here
    }
}

Make sure you isolate this to your custom post type as this action runs on all post types (i.e. pages, posts, other cpts). Not isolating your operation can get very very expensive on your system resources.