Why should not a Symfony2 bundle embed third-party libraries
Well, for one, It's counter-intuitive. Symfony Bundles are for packages of PHP functionality and you're talking about bundling up front-end libraries.
Secondly - why would it be easier? Things like bootstrap and jQuery are public resources to begin with - they don't need a distributable bundle to achieve high re-use. PHP resources are not public and therefore benefit from this type of system.
The chaos comes when two or more bundles uses the same 3rd party library but different versions. A user of your bundle won't be able to choose which library to include and therefore can't use both bundles at the time.
It's fine to store them in a bundle folder if your bundle is a standalone application, i.e. your application's main bundle. For example, SonataAdminBundle includes 3rd party libraries: bootstrap.css, qtip, famfamfam icons.
look at MopaBootstrapBundle https://github.com/phiamo/MopaBootstrapBundle it integrates TwitterBootstrap & jQuery lib for you, also HTML5BoilerPlate if you enable initializr addon.