### 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
if (p_config_file->has_section_key(EDITOR_NODE_CONFIG_SECTION, "center_split_offset")) {
		int center_split_offset = p_config_file->get_value(EDITOR_NODE_CONFIG_SECTION, "center_split_offset");
		center_split->set_split_offset(center_split_offset);
	}
	if (p_config_file->has_section_key(EDITOR_NODE_CONFIG_SECTION, "selected_bottom_panel_item")) {
		int selected_bottom_panel_item_idx = p_config_file->get_value(EDITOR_NODE_CONFIG_SECTION, "selected_bottom_panel_item");
		if (selected_bottom_panel_item_idx >= 0 && selected_bottom_panel_item_idx < bottom_panel_items.size()) {
			_bottom_panel_switch(true, selected_bottom_panel_item_idx);
		}
	}
	
	if (p_config_file->has_section_key(EDITOR_NODE_CONFIG_SECTION, "selected_default_debugger_tab_idx")) {
		int selected_default_debugger_tab_idx = p_config_file->get_value(EDITOR_NODE_CONFIG_SECTION, "selected_default_debugger_tab_idx");
		EditorDebuggerNode::get_singleton()->get_default_debugger()->switch_to_debugger(selected_default_debugger_tab_idx);
	}
	
	if (p_config_file->has_section_key(EDITOR_NODE_CONFIG_SECTION, "selected_main_editor_idx")) {
		int selected_main_editor_idx = p_config_file->get_value(EDITOR_NODE_CONFIG_SECTION, "selected_main_editor_idx");
		if (selected_main_editor_idx >= 0 && selected_main_editor_idx < main_editor_buttons.size()) {
			callable_mp(this, &EditorNode::editor_select).call_deferred(selected_main_editor_idx);
		}
	}
}
void EditorNode::_load_open_scenes_from_config(Ref<ConfigFile> p_layout) {