Is there a reliable way to show Drupal messages from JavaScript?
I'm using Nice messages module to replace every message with a popup in the corner of the screen.

https://drupal.org/project/nicemessages

It lets you choose if you want the messages of a status to stay visible until closed, or auto close after x seconds.
And add a handy "close all" if there are more than one.

If anything, check out how it works. It's a good starting point i guess.