### 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
r_style = 0;
	r_style_ex = WS_EX_WINDOWEDGE;
	if (p_main_window) {
		r_style_ex |= WS_EX_APPWINDOW;
		r_style |= WS_VISIBLE;
	}
	if (p_fullscreen || p_borderless) {
		r_style |= WS_POPUP; 
		if (p_fullscreen && p_multiwindow_fs) {
			r_style |= WS_BORDER; 
		}
	} else {
		if (p_resizable) {
			if (p_maximized) {
				r_style = WS_OVERLAPPEDWINDOW | WS_MAXIMIZE;
			} else {
				r_style = WS_OVERLAPPEDWINDOW;
			}
		} else {
			r_style = WS_OVERLAPPED | WS_CAPTION | WS_SYSMENU;
		}