### Godot version

Master (0ddd9c3e8f9088fa139e25b2903289d727073e12)

### System information

PopOS 22.04 - Intel integrated graphics - all backends

### Issue description

When there are popup windows in the editor, I cannot click on the "Confirm"/"Cancel" type buttons at the button. 

I have the issue both in the project manager (importing projects I can click on files etc. but cannot click "open") and when running the editor (cannot click "Save&Quit" etc.)

Sometimes the editor correctly highlights the buttons and I can use the arrow keys to navigate the buttons and "enter" to confirm my selection.

_I can navigate the editor closing dialogue with tab/arrow keys_
![Screenshot from 2023-01-16 14-24-06](https://user-images.githubusercontent.com/16521339/212774269-d784ea5e-5921-4460-9124-48978939c8e7.png)

_I can't navigate the project import dialogue with tab/arrow keys_
![Screenshot from 2023-01-16 14-29-00](https://user-images.githubusercontent.com/16521339/212774683-0a80795a-eed4-4e65-b2ca-3562c25d71fd.png)


### Steps to reproduce

Run the editor

### Minimal reproduction project

Reproducible in the project manager
_THREAD_SAFE_METHOD_
	ERR_FAIL_COND_V(!windows.has(p_window), Size2i());
	const WindowData &wd = windows[p_window];
	if (wd.fullscreen) {
		return wd.position;
	}
	XWindowAttributes xwa;
	XSync(x11_display, False);
	XGetWindowAttributes(x11_display, wd.x11_window, &xwa);
	int x = wd.position.x;
	int y = wd.position.y;
	Atom prop = XInternAtom(x11_display, "_NET_FRAME_EXTENTS", True);
	if (prop != None) {
		Atom type;
		int format;
		unsigned long len;
		unsigned long remaining;
		unsigned char *data = nullptr;
		if (XGetWindowProperty(x11_display, wd.x11_window, prop, 0, 4, False, AnyPropertyType, &type, &format, &len, &remaining, &data) == Success) {
			if (format == 32 && len == 4 && data) {
				long *extents = (long *)data;
				x -= extents[0]; 
				y -= extents[2]; 
			}
			XFree(data);
		}
	}
	return Size2i(x, y);
}
void DisplayServerX11::window_set_position(const Point2i &p_position, WindowID p_window) {