### 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
switch (p_screen) {
		case SCREEN_PRIMARY: {
			p_screen = get_primary_screen();
		} break;
		case SCREEN_OF_MAIN_WINDOW: {
			p_screen = window_get_current_screen(MAIN_WINDOW_ID);
		} break;
		default:
			break;
	}
	EnumSizeData data = { 0, p_screen, Size2() };
	EnumDisplayMonitors(nullptr, nullptr, _MonitorEnumProcSize, (LPARAM)&data);
	return data.size;
}
static BOOL CALLBACK _MonitorEnumProcUsableSize(HMONITOR hMonitor, HDC hdcMonitor, LPRECT lprcMonitor, LPARAM dwData) {
	EnumRectData *data = (EnumRectData *)dwData;
	if (data->count == data->screen) {
		MONITORINFO minfo;
		memset(&minfo, 0, sizeof(MONITORINFO));
		minfo.cbSize = sizeof(MONITORINFO);
		GetMonitorInfoA(hMonitor, &minfo);
		data->rect.position.x = minfo.rcWork.left;
		data->rect.position.y = minfo.rcWork.top;
		data->rect.size.x = minfo.rcWork.right - minfo.rcWork.left;
		data->rect.size.y = minfo.rcWork.bottom - minfo.rcWork.top;
	}
	data->count++;
	return TRUE;
}
static BOOL CALLBACK _MonitorEnumProcRefreshRate(HMONITOR hMonitor, HDC hdcMonitor, LPRECT lprcMonitor, LPARAM dwData) {