### 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
EditorFileDialog::set_default_display_mode((EditorFileDialog::DisplayMode)EDITOR_GET("filesystem/file_dialog/display_mode").operator int());
			bool theme_changed =
					EditorSettings::get_singleton()->check_changed_settings_in_group("interface/theme") ||
					EditorSettings::get_singleton()->check_changed_settings_in_group("interface/editor/font") ||
					EditorSettings::get_singleton()->check_changed_settings_in_group("interface/editor/main_font") ||
					EditorSettings::get_singleton()->check_changed_settings_in_group("interface/editor/code_font") ||
					EditorSettings::get_singleton()->check_changed_settings_in_group("text_editor/theme") ||
					EditorSettings::get_singleton()->check_changed_settings_in_group("text_editor/help/help") ||
					EditorSettings::get_singleton()->check_changed_settings_in_group("filesystem/file_dialog/thumbnail_size") ||
					EditorSettings::get_singleton()->check_changed_settings_in_group("run/output/font_size") ||
					EditorSettings::get_singleton()->check_changed_settings_in_group("interface/touchscreen/increase_scrollbar_touch_area") ||
					EditorSettings::get_singleton()->check_changed_settings_in_group("interface/touchscreen/scale_gizmo_handles");
			if (theme_changed) {
				theme = create_custom_theme(theme_base->get_theme());
				DisplayServer::set_early_window_clear_color_override(true, theme->get_color(SNAME("background"), SNAME("Editor")));
				theme_base->set_theme(theme);
				gui_base->set_theme(theme);
				get_window()->set_theme(theme);
				gui_base->add_theme_style_override("panel", gui_base->get_theme_stylebox(SNAME("Background"), SNAME("EditorStyles")));
				main_vbox->set_anchors_and_offsets_preset(Control::PRESET_FULL_RECT, Control::PRESET_MODE_MINSIZE, gui_base->get_theme_constant(SNAME("window_border_margin"), SNAME("Editor")));
				main_vbox->add_theme_constant_override("separation", gui_base->get_theme_constant(SNAME("top_bar_separation"), SNAME("Editor")));
				scene_root_parent->add_theme_style_override("panel", gui_base->get_theme_stylebox(SNAME("Content"), SNAME("EditorStyles")));
				bottom_panel->add_theme_style_override("panel", gui_base->get_theme_stylebox(SNAME("BottomPanel"), SNAME("EditorStyles")));
				tabbar_panel->add_theme_style_override("panel", gui_base->get_theme_stylebox(SNAME("tabbar_background"), SNAME("TabContainer")));
				scene_tabs->add_theme_constant_override("icon_max_width", gui_base->get_theme_constant(SNAME("class_icon_size"), SNAME("Editor")));
				scene_tab_add_ph->set_custom_minimum_size(scene_tab_add->get_minimum_size());
				main_menu->add_theme_style_override("hover", gui_base->get_theme_stylebox(SNAME("MenuHover"), SNAME("EditorStyles")));
			}
			scene_tabs->set_max_tab_width(int(EDITOR_GET("interface/scene_tabs/maximum_width")) * EDSCALE);
			_update_scene_tabs();