### 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_
	if (!windows.has(last_focused_window)) {
		return String(); 
	}
	String ret;
	if (!OpenClipboard(windows[last_focused_window].hWnd)) {
		ERR_FAIL_V_MSG("", "Unable to open clipboard.");
	}
	if (IsClipboardFormatAvailable(CF_UNICODETEXT)) {
		HGLOBAL mem = GetClipboardData(CF_UNICODETEXT);
		if (mem != nullptr) {
			LPWSTR ptr = (LPWSTR)GlobalLock(mem);
			if (ptr != nullptr) {
				ret = String::utf16((const char16_t *)ptr);
				GlobalUnlock(mem);