The original design of X had clients send drawing commands to the X server, basically treating the server as a remote Cairo/Skia-like 2D rasterizer, and subwindows were a cheap way to avoid pixel-level damage calculations. This was obviated in the common case by the Xdamage extension. Later use of windows as a rendering surface for shared client/server buffers was added with Xshm, then for device video buffers with Xv.

GTK3 got rid of windowed widgets because Keith Packard introduced the Xrender extension, which basically added 2D compositing to X, which was the last remaining use for subwindows for every widget.