### 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
if (!wd.no_focus && !wd.is_popup) {
			XSelectInput(x11_display, wd.x11_window, StructureNotifyMask);
		}
		
		
		{
			const long pid = OS::get_singleton()->get_process_id();
			Atom net_wm_pid = XInternAtom(x11_display, "_NET_WM_PID", False);
			if (net_wm_pid != None) {
				XChangeProperty(x11_display, wd.x11_window, net_wm_pid, XA_CARDINAL, 32, PropModeReplace, (unsigned char *)&pid, 1);
			}
		}
		long im_event_mask = 0;
		{
			XIEventMask all_event_mask;
			XSetWindowAttributes new_attr;
			new_attr.event_mask = KeyPressMask | KeyReleaseMask | ButtonPressMask |
					ButtonReleaseMask | EnterWindowMask |
					LeaveWindowMask | PointerMotionMask |
					Button1MotionMask |
					Button2MotionMask | Button3MotionMask |
					Button4MotionMask | Button5MotionMask |
					ButtonMotionMask | KeymapStateMask |
					ExposureMask | VisibilityChangeMask |
					StructureNotifyMask |
					SubstructureNotifyMask | SubstructureRedirectMask |
					FocusChangeMask | PropertyChangeMask |
					ColormapChangeMask | OwnerGrabButtonMask |
					im_event_mask;
			XChangeWindowAttributes(x11_display, wd.x11_window, CWEventMask, &new_attr);