### 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)
for (int j = 1; j < p_tile_set_atlas_source->get_alternative_tiles_count(coords); j++) {
			int alternative_tile = p_tile_set_atlas_source->get_alternative_tile_id(coords, j);
			if (coords != hovered_coords || alternative_tile != hovered_alternative) {
				TileData *tile_data = p_tile_set_atlas_source->get_tile_data(coords, alternative_tile);
				if (tile_data->get_terrain_set() != int(dummy_object->get("terrain_set"))) {
					
					p_canvas_item->draw_set_transform_matrix(p_transform);
					Rect2i rect = p_tile_atlas_view->get_alternative_tile_rect(coords, alternative_tile);
					p_canvas_item->draw_rect(rect, Color(0.0, 0.0, 0.0, 0.3));
					
					p_canvas_item->draw_set_transform_matrix(Transform2D());
					Rect2i texture_region = p_tile_atlas_view->get_alternative_tile_rect(coords, alternative_tile);
					Vector2i position = texture_region.get_center() + tile_data->get_texture_origin();
					Color color = Color(1, 1, 1);
					String text;
					if (tile_data->get_terrain_set() >= 0) {
						text = vformat("%d", tile_data->get_terrain_set());
					} else {
						text = "-";
					}
					Vector2 string_size = font->get_string_size(text, HORIZONTAL_ALIGNMENT_LEFT, -1, font_size);
					p_canvas_item->draw_string_outline(font, p_transform.xform(position) + Vector2i(-string_size.x / 2, string_size.y / 2), text, HORIZONTAL_ALIGNMENT_CENTER, string_size.x, font_size, 1, Color(0, 0, 0, 1));
					p_canvas_item->draw_string(font, p_transform.xform(position) + Vector2i(-string_size.x / 2, string_size.y / 2), text, HORIZONTAL_ALIGNMENT_CENTER, string_size.x, font_size, color);
				}
			}
		}
	}
	p_canvas_item->draw_set_transform_matrix(Transform2D());
}
void TileDataTerrainsEditor::forward_painting_atlas_gui_input(TileAtlasView *p_tile_atlas_view, TileSetAtlasSource *p_tile_set_atlas_source, const Ref<InputEvent> &p_event) {