### Godot version

4.0 9f68d06

### System information

Windows 10 x64

### Issue description

When changing any property of tile source, e.g. name:
![image](https://user-images.githubusercontent.com/2223172/219977766-9babbd6c-cd75-41a0-a167-fe6da039d05e.png)
This error appears in the output:
```
UndoRedo history mismatch: expected 0, got 2.
Set name
```
It means that there is an undo action that starts with a global object and continues with a scene one.

Only happens when the TileSet is built-in and it makes the changes to the tileset being registered as global, i.e. not related to its scene (which results in history inconsistency after closing the scene).

I did some debugging and the action comes from inspector, which edits TileSetAtlasSourceEditor and then TileSetAtlasSource. I don't know what exactly triggers it; the properties should be only set on TileSetAtlasSource.

### Steps to reproduce

1. Add scene
2. Add tilemap
3. Add tileset (don't save it to a file)
4. Edit tileset
5. Add atlas source (e.g. drop icon.svg)
6. Change atlas name
7. Observe output

### Minimal reproduction project

N/A
p_config_file->set_value(EDITOR_NODE_CONFIG_SECTION, "selected_main_editor_idx", Variant());
	}
}
void EditorNode::_load_central_editor_layout_from_config(Ref<ConfigFile> p_config_file) {
	
	bool has_active_tab = false;
	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()) {
			
			if (bottom_panel_items[selected_bottom_panel_item_idx].button->is_visible()) {
				_bottom_panel_switch(true, selected_bottom_panel_item_idx);
				has_active_tab = true;
			}
		}
	}
	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 (!has_active_tab) {
			bottom_panel_items[0].control->show(); 
			_bottom_panel_switch(false, 0);
		}
	}
	
	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);
	}