### Godot version

4.2 beta 2

### System information

Pop Os 22.04 lts 12th Gen Intel® Core™ i7-12700H × 20 NVIDIA RTX A2000 8GB 32.0  ram. Tested on Forward+ and Mobile

### Issue description

When painting a tile that is rotated or flipped, it looses its physics layer as demonstrated in this video:  

https://github.com/godotengine/godot/assets/33091666/c10f7325-838f-4112-b90d-0c3d9797d08f

Even though in the video I showed this only happening with one of the tiles, it happens with both of them as long as you rotate or flip it. 

### Steps to reproduce

1. Create a tilemap and a tileset
2. Create a physics layer and set collision_visibility_mode to force show. 
3. Assign just created physics layer to tiles
4. Paint the tiles and use rotate or flip tool. 

### Minimal reproduction project

[TileTest.zip](https://github.com/godotengine/godot/files/13067412/TileTest.zip)
TileData *tile_data = _get_tile_data(p_cell);
	ERR_FAIL_NULL(tile_data);
	bool valid;
	Variant value = tile_data->get(property, &valid);
	if (!valid) {
		return;
	}
	ERR_FAIL_COND(value.get_type() != Variant::VECTOR2I && value.get_type() != Variant::VECTOR2);
	Color color = Color(1.0, 1.0, 1.0);
	if (p_selected) {
		Color grid_color = EDITOR_GET("editors/tiles_editor/grid_color");
		Color selection_color = Color().from_hsv(Math::fposmod(grid_color.get_h() + 0.5, 1.0), grid_color.get_s(), grid_color.get_v(), 1.0);
		color = selection_color;
	}
	Ref<Texture2D> position_icon = TileSetEditor::get_singleton()->get_editor_theme_icon(SNAME("EditorPosition"));
	p_canvas_item->draw_texture(position_icon, p_transform.xform(Vector2(value)) - position_icon->get_size() / 2, color);
}
void TileDataYSortEditor::draw_over_tile(CanvasItem *p_canvas_item, Transform2D p_transform, TileMapCell p_cell, bool p_selected) {