Remove "Run in Background" message dialog
Polari's existing "Run in Background" behaviour hasn't proved to be all that popular. One reason for this, I think, is that people have certain expectations when it comes to IRC. They expect the client to exit when the window's closed. They also don't think of IRC as a type of messaging that is always on in the background, probably because it doesn't have any notion of persistence.
As a result of this, the "Run in Background" dialog that Polari show's can feel confusing and a bit like an imposition.
One viable solution would be to remove the Run in Background functionality entirely. I think that would be fine and would make most users happy.
An alternative would be to keep the Run in Background feature, but make it less invasive - to keep the check box in the app menu (which would default to off), but remove the dialog. This could cater to those users who do want Polari to be always running (although to be honest I haven't encountered anyone who wants this behaviour). In this model, "Running in the Background" would translate to the app continuing to run when the window is closed (we wouldn't autostart it).