That's not standard. If it's a one-window app, such as Skype, it should close the app. BareTorrent is also sort of a daemon process (where you often want it to live in the systray), and it follows standards. Minimize will put it in the system tray and close actually closes it. It's standard and feels intuitive.
I don't think so - I find this very subjective - I've always assumed that X just closes the window, even if it's a single window app. This is consistent, just some applications happen to also run in the background.
In case of Spotify, that window is the application. And the only window that the application has. Hitting X in that window should quit the application IMO.