Skype is the reason this behavior was popularized in VoIP apps. TeamSpeak and Mumble have a setting that allows this too, because people got used to Skype not shutting down after clicking "X".

Wasn't it msn messanger ?

Yes and Slack does the same.

Even AOL instant messenger did this. It would exit the window but still leave the application running with an icon in the systray area adjacent the clock.

Chat apps had that behavior since decades ago, ever since Windows95 got a systray. It's nothing new or special, it's kind of expected at this point.

Though I think here is a failure of Microsoft to improve the UI and use different symbols for closing the app and suspending it into the systray.

Either way, seems like a rather strict interpretation of 25.2. That said, I kind of welcome it. The principle of least surprise is something that should be much more strictly enforced and a lot of social apps make it way to easy to accidentally leak data into the public.

I would say close the window of chat app kill the ongoing chat session more surprising than not. The worst you should do is a prompt with yes/no and a checkbox to remember my decision when you do it the first time.