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On Windows SDL makes sure to use the screen coordinates of the client area for window positions.

    case WM_WINDOWPOSCHANGED:
        {
            RECT rect;
            int x, y;
            int w, h;
            
            if (data->in_border_change) {
                break;
            }

            if (!GetClientRect(hwnd, &rect) || IsRectEmpty(&rect)) {
                break;
            }
            ClientToScreen(hwnd, (LPPOINT) & rect);
            ClientToScreen(hwnd, (LPPOINT) & rect + 1);

            WIN_UpdateClipCursor(data->window);

            x = rect.left;
            y = rect.top;
            SDL_SendWindowEvent(data->window, SDL_WINDOWEVENT_MOVED, x, y);

On X11 the ConfigureNotify event gives the parent coordinates (which for SDL will always be screen coordinates) of the window, but SDL specifically adjusts them to account for the window border.

    case ConfigureNotify:{
#ifdef DEBUG_XEVENTS
            printf("window %p: ConfigureNotify! (position: %d,%d, size: %dx%d)\n", data,
                   xevent.xconfigure.x, xevent.xconfigure.y,
                   xevent.xconfigure.width, xevent.xconfigure.height);
#endif
            long border_left = 0;
            long border_top = 0;
            if (data->xwindow) {
                Atom _net_frame_extents = X11_XInternAtom(display, "_NET_FRAME_EXTENTS", 0);
                Atom type;
                int format;
                unsigned long nitems, bytes_after;
                unsigned char *property;
                if (X11_XGetWindowProperty(display, data->xwindow,
                        _net_frame_extents, 0, 16, 0,
                        XA_CARDINAL, &type, &format,
                        &nitems, &bytes_after, &property) == Success) {
                    if (type != None && nitems == 4)
                    {
                        border_left = ((long*)property)[0];
                        border_top = ((long*)property)[2];
                    }
                    X11_XFree(property);
                }
            }

            if (xevent.xconfigure.x != data->last_xconfigure.x ||
                xevent.xconfigure.y != data->last_xconfigure.y) {
                SDL_SendWindowEvent(data->window, SDL_WINDOWEVENT_MOVED,
                                    xevent.xconfigure.x - border_left,
                                    xevent.xconfigure.y - border_top);

As SDL_GetWindowPosition is supposed to return the position of the client area this adjustment seems incorrect and does not match Windows.