i think it would mostly be used for when you're away, when you come back to your computer you can see who has left a message for you. it would be easily over looked while chatting with other people, but you could have the option turned off when your status is "online"
the message would still open a convo window, i dont think you can turn that off (only with the ignore feature on the stuff plug plugin, but that's another story) but the convo window would be minimized as it always is, and you could make it so the task bar entry of that convo window would be hidden (which i know is possible) so it would seem as if there is no convo window, but there really would be, if you know what i mean. so then when you double click on the contact that has left you a message (which you see with a flashing icon) it shows the convo window that already would have been made with the message they left and also shows the task bar entry
ask me any questions of course if you dont understand what i mean
(just incase you dont know, a task bar entry is the rectangle that appears in the task bar (the bar usually at the bottom with the system tray etc) of a program or window, i dunno how to explain, hehe, but im sure you know what it is)
[edit] here's a lil thingy i made showing what it could look like: