With Settings → Tabs → Close window with last tab enabled:
With a single tab open, if the tab is open to a proper webpage, (e.g. wikipedia.org), pressing ⌘W correctly closes the tab and the window. If the tab is open to the Start Page (shown in the attached image), pressing ⌘W does nothing.

I expect that ⌘W should be sufficient to close a window with a single tab open to the Start Page.
0.99.133-beta
Sequoia (15)