### 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];
	switch (p_flag) {
		case WINDOW_FLAG_RESIZE_DISABLED: {
			wd.resize_disabled = p_enabled;
			_update_size_hints(p_window);
			XFlush(x11_display);
		} break;
		case WINDOW_FLAG_BORDERLESS: {
			Hints hints;
			Atom property;
			hints.flags = 2;
			hints.decorations = p_enabled ? 0 : 1;
			property = XInternAtom(x11_display, "_MOTIF_WM_HINTS", True);
			if (property != None) {
				XChangeProperty(x11_display, wd.x11_window, property, property, 32, PropModeReplace, (unsigned char *)&hints, 5);
			}
			
			window_set_size(window_get_size(p_window), p_window);
			wd.borderless = p_enabled;
			_update_window_mouse_passthrough(p_window);
		} break;
		case WINDOW_FLAG_ALWAYS_ON_TOP: {
			ERR_FAIL_COND_MSG(wd.transient_parent != INVALID_WINDOW_ID, "Can't make a window transient if the 'on top' flag is active.");
			if (p_enabled && wd.fullscreen) {