### 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)
TileData *tile_data = atlas_source->get_tile_data(neighbor_cell.get_atlas_coords(), neighbor_cell.alternative_tile);
					if (tile_data && tile_data->get_terrain_set() == p_terrain_set) {
						neighbor_tile_data = tile_data;
					}
				}
			}
			int terrain = neighbor_tile_data ? neighbor_tile_data->get_terrain_peering_bit(TileSet::CellNeighbor(E_overlapping.value)) : -1;
			if (!p_ignore_empty_terrains || terrain >= 0) {
				if (!terrain_count.has(terrain)) {
					terrain_count[terrain] = 0;
				}
				terrain_count[terrain] += 1;
			}
		}
		
		int max = 0;
		int max_terrain = -1;
		for (const KeyValue<int, int> &E_terrain_count : terrain_count) {
			if (E_terrain_count.value > max) {
				max = E_terrain_count.value;
				max_terrain = E_terrain_count.key;
			}
		}
		
		if (max > 0) {
			TerrainConstraint c = E_constraint;
			c.set_terrain(max_terrain);
			constraints.insert(c);
		}
	}