### 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 terrain = 0; terrain < get_terrains_count(terrain_set); terrain++) {
							bit_counts[terrain] = 0;
						}
						if (tile_data->get_terrain() >= 0) {
							bit_counts[tile_data->get_terrain()] += 10;
						}
						for (int terrain_bit = 0; terrain_bit < TileSet::CELL_NEIGHBOR_MAX; terrain_bit++) {
							TileSet::CellNeighbor cell_neighbor = TileSet::CellNeighbor(terrain_bit);
							if (is_valid_terrain_peering_bit(terrain_set, cell_neighbor)) {
								int terrain = tile_data->get_terrain_peering_bit(cell_neighbor);
								if (terrain >= 0) {
									if (terrain >= (int)bit_counts.size()) {
										WARN_PRINT(vformat("Invalid terrain peering bit: %d", terrain));
									} else {
										bit_counts[terrain] += 1;
									}
								}
							}
						}
						for (int terrain = 0; terrain < get_terrains_count(terrain_set); terrain++) {
							if ((bit_counts[terrain] > counts[terrain_set][terrain].count) || (bit_counts[terrain] == counts[terrain_set][terrain].count && tile_data->get_probability() > counts[terrain_set][terrain].probability)) {
								counts[terrain_set][terrain].count = bit_counts[terrain];
								counts[terrain_set][terrain].probability = tile_data->get_probability();
								counts[terrain_set][terrain].texture = atlas_source->get_texture();
								counts[terrain_set][terrain].region = atlas_source->get_tile_texture_region(tile_id);
							}
						}
					}
				}
			}