### 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(!windows.has(p_window));
	WindowData &wd = windows[p_window];
	int x = 0;
	int y = 0;
	if (!window_get_flag(WINDOW_FLAG_BORDERLESS, p_window)) {
		
		XSync(x11_display, False);
		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);
			}
		}
	}
	XMoveWindow(x11_display, wd.x11_window, p_position.x - x, p_position.y - y);
	_update_real_mouse_position(wd);
}
void DisplayServerX11::window_set_max_size(const Size2i p_size, WindowID p_window) {