### 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
for (KeyValue<WindowID, WindowData> &E : windows) {
		WindowData &wd = E.value;
		wd.block_mm = false;
		if ((p_old_driver == "wintab") && wintab_available && wd.wtctx) {
			wintab_WTEnable(wd.wtctx, false);
			wintab_WTClose(wd.wtctx);
			wd.wtctx = 0;
		}
		if ((p_new_driver == "wintab") && wintab_available) {
			wintab_WTInfo(WTI_DEFSYSCTX, 0, &wd.wtlc);
			wd.wtlc.lcOptions |= CXO_MESSAGES;
			wd.wtlc.lcPktData = PK_STATUS | PK_NORMAL_PRESSURE | PK_TANGENT_PRESSURE | PK_ORIENTATION;
			wd.wtlc.lcMoveMask = PK_STATUS | PK_NORMAL_PRESSURE | PK_TANGENT_PRESSURE;
			wd.wtlc.lcPktMode = 0;
			wd.wtlc.lcOutOrgX = 0;
			wd.wtlc.lcOutExtX = wd.wtlc.lcInExtX;
			wd.wtlc.lcOutOrgY = 0;
			wd.wtlc.lcOutExtY = -wd.wtlc.lcInExtY;
			wd.wtctx = wintab_WTOpen(wd.hWnd, &wd.wtlc, false);
			if (wd.wtctx) {
				wintab_WTEnable(wd.wtctx, true);
				AXIS pressure;
				if (wintab_WTInfo(WTI_DEVICES + wd.wtlc.lcDevice, DVC_NPRESSURE, &pressure)) {