No, the application won't see the passwords that have been marked using the Never Save This Password. Secondly, most of the nowadays forms are developed in such way that makes these apps useless due to security concerns.
There is also a page where you can see more details about this: http://www.nirsoft.net/utils/web_browser_password.html
Note: Also, make sure to update the application to the latest version, if you plan on using it for latest versions of the browsers.