The Bookmarklet (pop-up) injects itself into the page and sometimes the website security policy doesn't allow that and so for this purpose extension is better since it gets only the page URL as required info. For most cases the Bookmarklet is OK, I use it more often because it sticks to the account which means the short URL will be assigned to you so you can track clicks when needed (the extension will do that too in the upcoming new versions).

In the previous post I meant the Bookmarklet that is available in the user account ;) Thanks for your comment btw!