### 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
_THREAD_SAFE_METHOD_
	WindowID window_id = _create_window(p_mode, p_vsync_mode, p_flags, p_rect);
	ERR_FAIL_COND_V_MSG(window_id == INVALID_WINDOW_ID, INVALID_WINDOW_ID, "Failed to create sub window.");
	WindowData &wd = windows[window_id];
	if (p_flags & WINDOW_FLAG_RESIZE_DISABLED_BIT) {
		wd.resizable = false;
	}
	if (p_flags & WINDOW_FLAG_BORDERLESS_BIT) {
		wd.borderless = true;
	}
	if (p_flags & WINDOW_FLAG_ALWAYS_ON_TOP_BIT && p_mode != WINDOW_MODE_FULLSCREEN && p_mode != WINDOW_MODE_EXCLUSIVE_FULLSCREEN) {
		wd.always_on_top = true;
	}
	if (p_flags & WINDOW_FLAG_NO_FOCUS_BIT) {
		wd.no_focus = true;
	}
	if (p_flags & WINDOW_FLAG_MOUSE_PASSTHROUGH_BIT) {
		wd.mpass = true;
	}
	if (p_flags & WINDOW_FLAG_POPUP_BIT) {
		wd.is_popup = true;
	}
	
	HICON mainwindow_icon = (HICON)SendMessage(windows[MAIN_WINDOW_ID].hWnd, WM_GETICON, ICON_SMALL, 0);
	if (mainwindow_icon) {
		SendMessage(windows[window_id].hWnd, WM_SETICON, ICON_SMALL, (LPARAM)mainwindow_icon);