### 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_tab_move_left->set_flat(true);
	if (gui_base->is_layout_rtl()) {
		dock_tab_move_left->set_icon(theme->get_icon(SNAME("Forward"), SNAME("EditorIcons")));
	} else {
		dock_tab_move_left->set_icon(theme->get_icon(SNAME("Back"), SNAME("EditorIcons")));
	}
	dock_tab_move_left->set_focus_mode(Control::FOCUS_NONE);
	dock_tab_move_left->connect("pressed", callable_mp(this, &EditorNode::_dock_move_left));
	dock_hb->add_child(dock_tab_move_left);
	Label *dock_label = memnew(Label);
	dock_label->set_text(TTR("Dock Position"));
	dock_label->set_h_size_flags(Control::SIZE_EXPAND_FILL);
	dock_label->set_horizontal_alignment(HORIZONTAL_ALIGNMENT_CENTER);
	dock_hb->add_child(dock_label);
	dock_tab_move_right = memnew(Button);
	dock_tab_move_right->set_flat(true);
	if (gui_base->is_layout_rtl()) {
		dock_tab_move_right->set_icon(theme->get_icon(SNAME("Back"), SNAME("EditorIcons")));
	} else {
		dock_tab_move_right->set_icon(theme->get_icon(SNAME("Forward"), SNAME("EditorIcons")));
	}
	dock_tab_move_right->set_focus_mode(Control::FOCUS_NONE);
	dock_tab_move_right->connect("pressed", callable_mp(this, &EditorNode::_dock_move_right));
	dock_hb->add_child(dock_tab_move_right);
	dock_vb->add_child(dock_hb);
	dock_select = memnew(Control);
	dock_select->set_custom_minimum_size(Size2(128, 64) * EDSCALE);
	dock_select->connect("gui_input", callable_mp(this, &EditorNode::_dock_select_input));
	dock_select->connect("draw", callable_mp(this, &EditorNode::_dock_select_draw));
	dock_select->connect("mouse_exited", callable_mp(this, &EditorNode::_dock_popup_exit));