You're thinking only halfway
> similarly cmd+t closes a tab, wait cmd+w closes a tab not a window.
Because tabs are windows, and most multi-window-capable apps have the option to use tabs instead.
> and cmd+w in vlc does not close vlc
Again, in multi-window apps, closing the last window does not necessarily quit the app, but it's optional.
Consistent but optional, sounds inconsistent to me. Anyways that was 1 example, here's some more.
⌘R Reload in Safari; reply in Mail; reveal an alias's original in Finder
⌘L Address bar in browsers; message filter in Mail; clear to previous mark in Terminal.
⌘I File info in Finder; italics in text; inspector in Terminal.
I can keep going. This is not to say windows/osx is worse or better, just that claims of consistency are not suitable on either