### 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_undo_property(p_tile_set_atlas_source, vformat("%d:%d/%d/terrain", coords.x, coords.y, E.key.alternative_tile), dict["terrain"]);
							Array array = dict["terrain_peering_bits"];
							for (int i = 0; i < array.size(); i++) {
								TileSet::CellNeighbor bit = TileSet::CellNeighbor(i);
								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();
				} else if (drag_type == DRAG_TYPE_PAINT_TERRAIN_BITS) {
					Dictionary painted = Dictionary(drag_painted_value);
					int terrain_set = int(painted["terrain_set"]);
					int terrain = int(painted["terrain"]);
					undo_redo->create_action(TTR("Painting Terrain"));
					for (KeyValue<TileMapCell, Variant> &E : drag_modified) {
						Dictionary dict = E.value;
						Vector2i coords = E.key.get_atlas_coords();
						undo_redo->add_do_property(p_tile_set_atlas_source, vformat("%d:%d/%d/terrain", coords.x, coords.y, E.key.alternative_tile), terrain);
						undo_redo->add_undo_property(p_tile_set_atlas_source, vformat("%d:%d/%d/terrain", coords.x, coords.y, E.key.alternative_tile), dict["terrain"]);
						Array array = dict["terrain_peering_bits"];
						for (int i = 0; i < array.size(); i++) {
							TileSet::CellNeighbor bit = TileSet::CellNeighbor(i);
							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)) {