### 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)
if (tile_set->is_valid_terrain_peering_bit(terrain_set, bit)) {
								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.key.alternative_tile), terrain);
							}
							if (tile_set->is_valid_terrain_peering_bit(dict["terrain_set"], bit)) {
								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.key.alternative_tile), array[i]);
							}
						}
					}
					undo_redo->commit_action(false);
					drag_type = DRAG_TYPE_NONE;
					accept_event();
				}
			}
		}
	}
}
void TileDataTerrainsEditor::draw_over_tile(CanvasItem *p_canvas_item, Transform2D p_transform, TileMapCell p_cell, bool p_selected) {
	TileData *tile_data = _get_tile_data(p_cell);
	ERR_FAIL_NULL(tile_data);
	tile_set->draw_terrains(p_canvas_item, p_transform, tile_data);
}
void TileDataTerrainsEditor::_notification(int p_what) {
	switch (p_what) {
		case NOTIFICATION_ENTER_TREE:
		case NOTIFICATION_THEME_CHANGED: {
			picker_button->set_icon(get_editor_theme_icon(SNAME("ColorPick")));
		} break;
	}
}
TileDataTerrainsEditor::TileDataTerrainsEditor() {