Can I return an object on which a function is applied?
Looks good to me, if you always want those 3 params and never want to send anything else.

Otherwise, you could improve it by receiving the non-mandatory params in an options object:

"use strict";
var initiate_shop = function(container_id, options) {
    var default_settings = {
            containerID     : container_id,
            first           : false,
            perPage         : 5,
            '...'           : '...',
            callback        : function(pages){
                current_page = pages.current;
                total_pages = pages.count;
            }
        },
        settings = $.extend(default_settings, options);
    return $(shop_navigation).jPages(settings);
};
// ...
initiate_shop('outputCell', {
    perPage:     10,
    first:       true
});


Related (hows 3 ways to assign default values to parameters):
https://stackoverflow.com/a/3672142/148412