### 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
WindowRect.left,
				WindowRect.top,
				WindowRect.right - WindowRect.left,
				WindowRect.bottom - WindowRect.top,
				nullptr,
				nullptr,
				hInstance,
				
				
				
				reinterpret_cast<void *>(&wd));
		if (!wd.hWnd) {
			MessageBoxW(nullptr, L"Window Creation Error.", L"ERROR", MB_OK | MB_ICONEXCLAMATION);
			windows.erase(id);
			ERR_FAIL_V_MSG(INVALID_WINDOW_ID, "Failed to create Windows OS window.");
		}
		if (p_mode == WINDOW_MODE_FULLSCREEN || p_mode == WINDOW_MODE_EXCLUSIVE_FULLSCREEN) {
			wd.fullscreen = true;
			if (p_mode == WINDOW_MODE_FULLSCREEN) {
				wd.multiwindow_fs = true;
			}
		}
		if (p_mode != WINDOW_MODE_FULLSCREEN && p_mode != WINDOW_MODE_EXCLUSIVE_FULLSCREEN) {
			wd.pre_fs_valid = true;
		}
		if (is_dark_mode_supported() && dark_title_available) {
			BOOL value = is_dark_mode();
			::DwmSetWindowAttribute(wd.hWnd, DWMWA_USE_IMMERSIVE_DARK_MODE, &value, sizeof(value));
		}
#ifdef VULKAN_ENABLED