I thought I explained it very very clearly but I will try again..
My understanding of "system volume control" - app may adjust it's sound output but after it leaves the app, it still passes through the "global" or "system" volume control. So, if "system volume", is muted, no app should be able to make any sound. Something like what a mechanical volume control knob would do. I could be wrong but I believe that's what everybody's understanding of "system volume" should be.
In reality - system sound is "muted", volume icon in the menu bar indicate that. Start a Skype call, and it makes it's ring sound, then you can hear a conversation, and system sound icon in the menu bar shows volume increased (without manually adjusting anything!).
End the Skype call, and volume (system volume!!!) automatically returns back to "muted".
As far as I understand, it cannot be changed by any setting in Skype (and confirmed by Skype support chat, it's just how Skype works, and they think it's correct), sound output is "same as system", notification sounds are disabled, and there are no other settings.
Now, it seems obvious that OS allows application Skype to mess with the "global" volume control which is a nonsense in my understanding. Computer with system volume muted, should make no sound, ever. However, like everything in macOS, there probably is a setting somewhere which can allow/disallow this.
Skype is an example, even it's so far the only application I have noticed violating the system volume setting.