Window transparency is available on all major platforms, and there are cross platform libs which support it, such as SDL3: https://wiki.libsdl.org/SDL3/SDL_WINDOW_TRANSPARENT (for rendering, making underlying windows visible where window surface pixels are transparent), https://wiki.libsdl.org/SDL3/SDL_SetWindowShape (for input, making pointer events pass to underlying windows where surface pixels are fully transparent)
I (ab)use it in my image (pre)viewer to have image presentation area always fitting image during pan&zoom without window borders limiting it, while having underlying windows visible outside of it (transparent fullscreen overlay): https://github.com/shatsky/lightning-image-viewer