How do I close only one Google Chrome window in macOS using mouse?
File → Close Window (⇧⌘W).

⌘W closes the tab which will close the window if this is the last tab, but ⇧⌘W closes the window containing any number of tabs.

This menu and shortcut is standard macOS working in all tabbed apps implementing macOS tabs, and Google Chrome has applied this shortcut to their tab implementation.