### Godot version

4.0.beta12

### System information

Windows 11, RTX 3080

### Issue description

When a Window Node is created with it's Transparent flag set to true and Project Settings --> Display --> Window --> Subwindows --> Embed Subwindows is false, the Window has a black background. By cycling the transparent flag from false and back to true again, during runtime, the window's background then becomes transparent. 

### Steps to reproduce

Attempt to create a Non-embedded Subwindow with a transparent background using the appropriate flags. 

### Minimal reproduction project

Note: this project is from Reddit user [gongpha](https://www.reddit.com/user/gongpha/) and his Reddit post [Learning a Godot 4.0 Window node](https://www.reddit.com/r/godot/comments/xr8yxn/learning_a_godot_40_window_node/)

https://github.com/gongpha/godot4-window-test
GetWindowRect(hWnd, &wrect);
				window_rect = Rect2i(wrect.left, wrect.top, wrect.right - wrect.left, wrect.bottom - wrect.top);
				window_rect.position -= _get_screens_origin();
			}
			WINDOWPOS *window_pos_params = (WINDOWPOS *)lParam;
			WindowData &window = windows[window_id];
			bool rect_changed = false;
			if (!(window_pos_params->flags & SWP_NOSIZE) || window_pos_params->flags & SWP_FRAMECHANGED) {
				int screen_id = window_get_current_screen(window_id);
				Size2i screen_size = screen_get_size(screen_id);
				Point2i screen_position = screen_get_position(screen_id);
				window.maximized = false;
				window.minimized = false;
				window.fullscreen = false;
				if (IsIconic(hWnd)) {
					window.minimized = true;
				} else if (IsZoomed(hWnd)) {
					window.maximized = true;
				} else if (window_rect.position == screen_position && window_rect.size == screen_size) {
					window.fullscreen = true;
				}
				if (!window.minimized) {
					window.width = window_client_rect.size.width;
					window.height = window_client_rect.size.height;
					rect_changed = true;
				}
#if defined(VULKAN_ENABLED)
				if (context_vulkan && window.context_created) {
					
					context_vulkan->window_resize(window_id, window.width, window.height);