### 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
bottom_panel_updating = true;
		for (int i = 0; i < bottom_panel_items.size(); i++) {
			bottom_panel_items[i].button->set_pressed(i == p_idx);
			bottom_panel_items[i].control->set_visible(i == p_idx);
		}
		if (EditorDebuggerNode::get_singleton() == bottom_panel_items[p_idx].control) {
			
			bottom_panel->add_theme_style_override("panel", gui_base->get_theme_stylebox(SNAME("BottomPanelDebuggerOverride"), SNAME("EditorStyles")));
		} else {
			bottom_panel->add_theme_style_override("panel", gui_base->get_theme_stylebox(SNAME("BottomPanel"), SNAME("EditorStyles")));
		}
		center_split->set_dragger_visibility(SplitContainer::DRAGGER_VISIBLE);
		center_split->set_collapsed(false);
		if (bottom_panel_raise->is_pressed()) {
			top_split->hide();
		}
		bottom_panel_raise->show();
	} else {
		bottom_panel->add_theme_style_override("panel", gui_base->get_theme_stylebox(SNAME("BottomPanel"), SNAME("EditorStyles")));
		bottom_panel_items[p_idx].button->set_pressed(false);
		bottom_panel_items[p_idx].control->set_visible(false);
		center_split->set_dragger_visibility(SplitContainer::DRAGGER_HIDDEN);
		center_split->set_collapsed(true);
		bottom_panel_raise->hide();
		if (bottom_panel_raise->is_pressed()) {
			top_split->show();
		}
	}
}
void EditorNode::set_docks_visible(bool p_show) {