Using YUI Loader's onProgress callback to load 3rd party libraries as custom modules. Still needs a little bit of tweaking...

3rd_party_loader.js

var module = {
    exports : {}
};
var exports = {};

YUI({
    modules     : {
        'jquery'        : {
            fullpath        : 'http://code.jquery.com/jquery-1.10.1.min.js'
        },
        'lodash'        : {
            fullpath        : 'http://cdnjs.cloudflare.com/ajax/libs/lodash.js/1.3.1/lodash.min.js'
        }
    },
    onProgress  : function(e) {
        console.log('onProgress', e, module.exports);

        // create dynamic, 3rd-party modules
        switch(e.name) {
            case 'jquery' :
                (function() {
                    var clone;
                    
                    YUI.add('jquery', function(Y) {
                      // create a clone ONLY once
                      if (!clone) {
                          clone           = Y.clone(module.exports, true);
                          module.exports  = {};
                      }
  
                      Y.namespace('3rd_party')
                          .jQuery = clone;
                    }, '1.10.1');
                })();
            break;

            case 'lodash' :
                (function() {
                    var clone;

                    YUI.add('lodash', function(Y) {
                        // create a clone ONLY once
                        if (!clone) {
                            clone   = Y.clone(exports, true);
                            exports = {};
                        }
    
                        Y.namespace('3rd_party')
                            .lodash = clone;
                    }, '1.3.1');
                })();
            break;
        }                   
    }
}).use('jquery', 'lodash',
    function(Y) {
        var $, _;

        $   = Y['3rd_party'].jQuery;
        _   = Y['3rd_party'].lodash._;
        
        $('<h1>jQuery ' + $.prototype.jquery + ' in YUI! It works!</h1>')
            .appendTo('body');

        $('<h1>Lo-Dash ' +  _.VERSION +  ' in YUI! It works!</h1>')
            .appendTo('body');
    });