### 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)
undo_redo->add_do_property(p_tile_set_atlas_source, vformat("%d:%d/%d/terrains_peering_bit/" + String(TileSet::CELL_NEIGHBOR_ENUM_TO_TEXT[i]), coords.x, coords.y, E.alternative_tile), terrain);
									undo_redo->add_undo_property(p_tile_set_atlas_source, vformat("%d:%d/%d/terrains_peering_bit/" + String(TileSet::CELL_NEIGHBOR_ENUM_TO_TEXT[i]), coords.x, coords.y, E.alternative_tile), tile_data->get_terrain_peering_bit(bit));
								}
							}
						}
					}
					undo_redo->commit_action(true);
					drag_type = DRAG_TYPE_NONE;
					accept_event();
				}
			}
		}
	}
}
void TileDataTerrainsEditor::forward_painting_alternatives_gui_input(TileAtlasView *p_tile_atlas_view, TileSetAtlasSource *p_tile_set_atlas_source, const Ref<InputEvent> &p_event) {
	Ref<InputEventMouseMotion> mm = p_event;
	if (mm.is_valid()) {
		if (drag_type == DRAG_TYPE_PAINT_TERRAIN_SET) {
			Vector3i tile = p_tile_atlas_view->get_alternative_tile_at_pos(mm->get_position());
			Vector2i coords = Vector2i(tile.x, tile.y);
			int alternative_tile = tile.z;
			if (coords != TileSetSource::INVALID_ATLAS_COORDS) {
				TileMapCell cell;
				cell.source_id = 0;
				cell.set_atlas_coords(coords);
				cell.alternative_tile = alternative_tile;
				TileData *tile_data = p_tile_set_atlas_source->get_tile_data(coords, alternative_tile);
				if (!drag_modified.has(cell)) {
					Dictionary dict;