### 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)
const Ref<TileSet> &tile_set = tile_map_node->get_tileset();
	if (!tile_set.is_valid()) {
		return RBSet<TerrainConstraint>();
	}
	ERR_FAIL_INDEX_V(p_terrain_set, tile_set->get_terrain_sets_count(), RBSet<TerrainConstraint>());
	
	RBSet<TerrainConstraint> dummy_constraints;
	for (const Vector2i &E : p_painted) {
		for (int i = 0; i < TileSet::CELL_NEIGHBOR_MAX; i++) { 
			TileSet::CellNeighbor bit = TileSet::CellNeighbor(i);
			if (tile_set->is_valid_terrain_peering_bit(p_terrain_set, bit)) {
				dummy_constraints.insert(TerrainConstraint(tile_map_node, E, bit, -1));
			}
		}
	}
	
	RBSet<TerrainConstraint> constraints;
	for (const TerrainConstraint &E_constraint : dummy_constraints) {
		HashMap<int, int> terrain_count;
		
		HashMap<Vector2i, TileSet::CellNeighbor> overlapping_terrain_bits = E_constraint.get_overlapping_coords_and_peering_bits();
		for (const KeyValue<Vector2i, TileSet::CellNeighbor> &E_overlapping : overlapping_terrain_bits) {
			TileData *neighbor_tile_data = nullptr;
			TileMapCell neighbor_cell = get_cell(E_overlapping.key);
			if (neighbor_cell.source_id != TileSet::INVALID_SOURCE) {
				Ref<TileSetSource> source = tile_set->get_source(neighbor_cell.source_id);
				Ref<TileSetAtlasSource> atlas_source = source;
				if (atlas_source.is_valid()) {