### Godot version

3.5.2.stable, 4.0.1.stable

### System information

Arch Linux

### Issue description

When the `Show Hidden Files` property is enabled in the Editor Settings:
![image](https://user-images.githubusercontent.com/6501975/226908540-8e70e520-3dcd-46e4-beaf-103ac176c1de.png)
Any `FileDialog` nodes from the project will inherit this setting, and their `Show Hidden Files` property is set to true everytime the scene is re-opened:

https://user-images.githubusercontent.com/6501975/226909135-a8fafdf7-ca36-40aa-b69a-a7baf2d7ae4f.mp4


This occurs on 3.5.2 as well.

### Steps to reproduce

- Enable `Show Hidden Files` property in the Editor Settings:
    - Reload Godot for the bug to occur
- Create a FileDialog node, and set it's `Show Hidden Files` property to false
- Save and close the scene, and reopen it
- The `Show Hidden Files` property is reset to true.

### Minimal reproduction project

N/A
EditorPlugin::AfterGUIInput after = EditorPlugin::AFTER_GUI_INPUT_PASS;
	for (int i = 0; i < plugins_list.size(); i++) {
		if ((!serve_when_force_input_enabled) && plugins_list[i]->is_input_event_forwarding_always_enabled()) {
			continue;
		}
		EditorPlugin::AfterGUIInput current_after = plugins_list[i]->forward_3d_gui_input(p_camera, p_event);
		if (current_after == EditorPlugin::AFTER_GUI_INPUT_STOP) {
			after = EditorPlugin::AFTER_GUI_INPUT_STOP;
		}
		if (after != EditorPlugin::AFTER_GUI_INPUT_STOP && current_after == EditorPlugin::AFTER_GUI_INPUT_CUSTOM) {
			after = EditorPlugin::AFTER_GUI_INPUT_CUSTOM;
		}
	}
	return after;
}
void EditorPluginList::forward_canvas_draw_over_viewport(Control *p_overlay) {
	for (int i = 0; i < plugins_list.size(); i++) {
		plugins_list[i]->forward_canvas_draw_over_viewport(p_overlay);
	}
}
void EditorPluginList::forward_canvas_force_draw_over_viewport(Control *p_overlay) {
	for (int i = 0; i < plugins_list.size(); i++) {
		plugins_list[i]->forward_canvas_force_draw_over_viewport(p_overlay);
	}
}
void EditorPluginList::forward_3d_draw_over_viewport(Control *p_overlay) {