### 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
dock_select->set_v_size_flags(Control::SIZE_EXPAND_FILL);
	dock_vb->add_child(dock_select);
	if (!SceneTree::get_singleton()->get_root()->is_embedding_subwindows() && EDITOR_GET("interface/multi_window/enable")) {
		dock_float = memnew(Button);
		dock_float->set_icon(theme->get_icon("MakeFloating", "EditorIcons"));
		dock_float->set_text(TTR("Make Floating"));
		dock_float->set_focus_mode(Control::FOCUS_NONE);
		dock_float->set_h_size_flags(Control::SIZE_SHRINK_CENTER);
		dock_float->connect("pressed", callable_mp(this, &EditorNode::_dock_make_selected_float));
		dock_vb->add_child(dock_float);
	}
	dock_select_popup->reset_size();
	for (int i = 0; i < DOCK_SLOT_MAX; i++) {
		dock_slot[i]->set_custom_minimum_size(Size2(170, 0) * EDSCALE);
		dock_slot[i]->set_v_size_flags(Control::SIZE_EXPAND_FILL);
		dock_slot[i]->set_popup(dock_select_popup);
		dock_slot[i]->connect("pre_popup_pressed", callable_mp(this, &EditorNode::_dock_pre_popup).bind(i));
		dock_slot[i]->set_drag_to_rearrange_enabled(true);
		dock_slot[i]->set_tabs_rearrange_group(1);
		dock_slot[i]->connect("tab_changed", callable_mp(this, &EditorNode::_dock_tab_changed));
		dock_slot[i]->set_use_hidden_tabs_for_min_size(true);
	}
	editor_layout_save_delay_timer = memnew(Timer);
	add_child(editor_layout_save_delay_timer);
	editor_layout_save_delay_timer->set_wait_time(0.5);
	editor_layout_save_delay_timer->set_one_shot(true);
	editor_layout_save_delay_timer->connect("timeout", callable_mp(this, &EditorNode::_save_editor_layout));
	top_split = memnew(VSplitContainer);
	center_split->add_child(top_split);
	top_split->set_v_size_flags(Control::SIZE_EXPAND_FILL);