Settings dressed like About: the teaser’s stripe across the top, and only the window buttons it needs, small, as About and the panel have them. The sidebar and every pane stay as built. Hover the buttons to see their glyphs; click the window to see it in front or behind.
Proposed
The stripe runs across the top, 16 pt, as on About and the site, in place of the title bar. Its bright tones are lifted toward the window in light mode, as About’s are. It’s also where you drag the window.
No title bar, and no “Settings” title. The pane’s name already heads the form. The window is still called Settings in the Window menu, Mission Control and the Dock’s window list.
Small window buttons in the sidebar’s top corner, under the stripe, above Search, at the size About and the panel use. A, close only (recommended): Settings is set and closed, like About. B, close and minimize, for keeping it a click away. Zoom goes in both: one window size fits every pane (0.99.0), and the window stays resizable from its edges.
Closing is as now: the red button or ⌘W. The window keeps its size and place.
The sidebar, search, panes and their system greys don’t change. The stripe is the one touch of the app’s palette, as About’s is.
Open questions
A or B: close only, or close and minimize? (A recommended)
Drop the “Settings” title with the title bar? (yes/no; recommended yes, since the pane’s name heads the form)