It doesn't render them. Framebuffer native apps back then didn't have enough memory bandwidth to change every pixel every frame either. They just changed the ones that changed. You'd probably still let the compositor use the GPU to drag windows around. They had that back then too, it was called accelerated blitting.

GL based widget toolkits only render the needed pixels too. It's good for saving battery but isn't enough by itself as it only works until the app genuinely needs to repaint the entire window. Think a text editor or IDE switching to a different file.