I added support for showing messages on top of other programs for private messages in mIRGGI. Should work on 2nd and 3rd ed, not tested that much.
Also, there are no vibrations, sounds, light going on or dot turning red if the action on a channel is just a join, topic change, mode change etc. Only messages will cause notifications.
Oh, and at the moment the query window that is selected in mIRGGI won't cause messages, even if mIRGGI is in the background. This will be fixed in the next version, as well as a setting for the notification.