### 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
XGetWindowAttributes(x11_display, wd_parent.x11_window, &xwa);
		
		
		
		if (!wd_window.no_focus && !wd_window.is_popup && wd_window.focused) {
			if ((xwa.map_state == IsViewable) && !wd_parent.no_focus && !wd_window.is_popup) {
				XSetInputFocus(x11_display, wd_parent.x11_window, RevertToPointerRoot, CurrentTime);
			}
		}
	} else {
		ERR_FAIL_COND(!windows.has(p_parent));
		ERR_FAIL_COND_MSG(prev_parent != INVALID_WINDOW_ID, "Window already has a transient parent");
		WindowData &wd_parent = windows[p_parent];
		wd_window.transient_parent = p_parent;
		wd_parent.transient_children.insert(p_window);
		XSetTransientForHint(x11_display, wd_window.x11_window, wd_parent.x11_window);
	}
}
void DisplayServerX11::_update_size_hints(WindowID p_window) {
	WindowData &wd = windows[p_window];
	WindowMode window_mode = window_get_mode(p_window);
	XSizeHints *xsh = XAllocSizeHints();
	
	xsh->flags |= PPosition | PSize;
	xsh->x = wd.position.x;
	xsh->y = wd.position.y;
	xsh->width = wd.size.width;
	xsh->height = wd.size.height;
	if (window_mode == WINDOW_MODE_FULLSCREEN || window_mode == WINDOW_MODE_EXCLUSIVE_FULLSCREEN) {