### 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
for (int i = 0; i < bottom_panel_items.size(); i++) {
		if (bottom_panel_items[i].control->is_visible()) {
			_bottom_panel_switch(false, i);
			break;
		}
	}
}
void EditorNode::make_bottom_panel_item_visible(Control *p_item) {
	for (int i = 0; i < bottom_panel_items.size(); i++) {
		if (bottom_panel_items[i].control == p_item) {
			_bottom_panel_switch(true, i);
			break;
		}
	}
}
void EditorNode::raise_bottom_panel_item(Control *p_item) {
	for (int i = 0; i < bottom_panel_items.size(); i++) {
		if (bottom_panel_items[i].control == p_item) {
			bottom_panel_items[i].button->move_to_front();
			SWAP(bottom_panel_items.write[i], bottom_panel_items.write[bottom_panel_items.size() - 1]);
			break;
		}
	}
	for (int i = 0; i < bottom_panel_items.size(); i++) {
		bottom_panel_items[i].button->disconnect("toggled", callable_mp(this, &EditorNode::_bottom_panel_switch));
		bottom_panel_items[i].button->connect("toggled", callable_mp(this, &EditorNode::_bottom_panel_switch).bind(i));
	}
}
void EditorNode::remove_bottom_panel_item(Control *p_item) {