### 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
_set_wm_maximized(p_window, true);
			}
			Atom wm_state = XInternAtom(x11_display, "_NET_WM_STATE", False);
			Atom wm_above = XInternAtom(x11_display, "_NET_WM_STATE_ABOVE", False);
			XClientMessageEvent xev;
			memset(&xev, 0, sizeof(xev));
			xev.type = ClientMessage;
			xev.window = wd.x11_window;
			xev.message_type = wm_state;
			xev.format = 32;
			xev.data.l[0] = p_enabled ? _NET_WM_STATE_ADD : _NET_WM_STATE_REMOVE;
			xev.data.l[1] = wm_above;
			xev.data.l[3] = 1;
			XSendEvent(x11_display, DefaultRootWindow(x11_display), False, SubstructureRedirectMask | SubstructureNotifyMask, (XEvent *)&xev);
			if (!p_enabled && !wd.fullscreen) {
				_set_wm_maximized(p_window, false);
			}
			wd.on_top = p_enabled;
		} break;
		case WINDOW_FLAG_TRANSPARENT: {
			wd.layered_window = p_enabled;
		} break;
		case WINDOW_FLAG_NO_FOCUS: {
			wd.no_focus = p_enabled;
		} break;
		case WINDOW_FLAG_MOUSE_PASSTHROUGH: {
			wd.mpass = p_enabled;
			_update_window_mouse_passthrough(p_window);
		} break;
		case WINDOW_FLAG_POPUP: {