### 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
wd.height = h;
#if defined(VULKAN_ENABLED)
	if (context_vulkan) {
		context_vulkan->window_resize(p_window, w, h);
	}
#endif
#if defined(GLES3_ENABLED)
	if (gl_manager) {
		gl_manager->window_resize(p_window, w, h);
	}
#endif
	RECT rect;
	GetWindowRect(wd.hWnd, &rect);
	if (!wd.borderless) {
		RECT crect;
		GetClientRect(wd.hWnd, &crect);
		w += (rect.right - rect.left) - (crect.right - crect.left);
		h += (rect.bottom - rect.top) - (crect.bottom - crect.top);
	}
	MoveWindow(wd.hWnd, rect.left, rect.top, w, h, TRUE);
	
	if (mouse_mode == MOUSE_MODE_CONFINED || mouse_mode == MOUSE_MODE_CONFINED_HIDDEN) {
		RECT crect;
		GetClientRect(wd.hWnd, &crect);
		ClientToScreen(wd.hWnd, (POINT *)&crect.left);
		ClientToScreen(wd.hWnd, (POINT *)&crect.right);
		ClipCursor(&crect);
	}
}
Size2i DisplayServerWindows::window_get_size(WindowID p_window) const {