### 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
int center_split_offset = center_split->get_split_offset();
	p_config_file->set_value(EDITOR_NODE_CONFIG_SECTION, "center_split_offset", center_split_offset);
	int selected_bottom_panel_item_idx = -1;
	for (int i = 0; i < bottom_panel_items.size(); i++) {
		if (bottom_panel_items[i].button->is_pressed()) {
			selected_bottom_panel_item_idx = i;
			break;
		}
	}
	if (selected_bottom_panel_item_idx != -1) {
		p_config_file->set_value(EDITOR_NODE_CONFIG_SECTION, "selected_bottom_panel_item", selected_bottom_panel_item_idx);
	} else {
		p_config_file->set_value(EDITOR_NODE_CONFIG_SECTION, "selected_bottom_panel_item", Variant());
	}
	
	int selected_default_debugger_tab_idx = EditorDebuggerNode::get_singleton()->get_default_debugger()->get_current_debugger_tab();
	p_config_file->set_value(EDITOR_NODE_CONFIG_SECTION, "selected_default_debugger_tab_idx", selected_default_debugger_tab_idx);
	
	int selected_main_editor_idx = -1;
	for (int i = 0; i < main_editor_buttons.size(); i++) {
		if (main_editor_buttons[i]->is_pressed()) {
			selected_main_editor_idx = i;
			break;
		}
	}
	if (selected_main_editor_idx != -1) {
		p_config_file->set_value(EDITOR_NODE_CONFIG_SECTION, "selected_main_editor_idx", selected_main_editor_idx);
	} else {