### 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
MDT_Effective_DPI = 0,
	MDT_Angular_DPI = 1,
	MDT_Raw_DPI = 2,
	MDT_Default = MDT_Effective_DPI
};
static int QueryDpiForMonitor(HMONITOR hmon, _MonitorDpiType dpiType = MDT_Default) {
	int dpiX = 96, dpiY = 96;
	static HMODULE Shcore = nullptr;
	typedef HRESULT(WINAPI * GetDPIForMonitor_t)(HMONITOR hmonitor, _MonitorDpiType dpiType, UINT * dpiX, UINT * dpiY);
	static GetDPIForMonitor_t getDPIForMonitor = nullptr;
	if (Shcore == nullptr) {
		Shcore = LoadLibraryW(L"Shcore.dll");
		getDPIForMonitor = Shcore ? (GetDPIForMonitor_t)GetProcAddress(Shcore, "GetDpiForMonitor") : nullptr;
		if ((Shcore == nullptr) || (getDPIForMonitor == nullptr)) {
			if (Shcore) {