### 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
ERR_FAIL_COND(!windows.has(p_id));
	ERR_FAIL_COND_MSG(p_id == MAIN_WINDOW_ID, "Main window can't be deleted");
	popup_close(p_id);
	WindowData &wd = windows[p_id];
	DEBUG_LOG_X11("delete_sub_window: %lu (%u) \n", wd.x11_window, p_id);
	while (wd.transient_children.size()) {
		window_set_transient(*wd.transient_children.begin(), INVALID_WINDOW_ID);
	}
	if (wd.transient_parent != INVALID_WINDOW_ID) {
		window_set_transient(p_id, INVALID_WINDOW_ID);
	}
#ifdef VULKAN_ENABLED
	if (context_vulkan) {
		context_vulkan->window_destroy(p_id);
	}
#endif
#ifdef GLES3_ENABLED
	if (gl_manager) {
		gl_manager->window_destroy(p_id);
	}
#endif
	XUnmapWindow(x11_display, wd.x11_window);
	XDestroyWindow(x11_display, wd.x11_window);
	if (wd.xic) {
		XDestroyIC(wd.xic);
		wd.xic = nullptr;
	}
	windows.erase(p_id);
}
int64_t DisplayServerX11::window_get_native_handle(HandleType p_handle_type, WindowID p_window) const {