### 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 (cell.source_id != TileSet::INVALID_SOURCE) {
				Ref<TileSetSource> source = tile_set->get_source(cell.source_id);
				Ref<TileSetAtlasSource> atlas_source = source;
				if (atlas_source.is_valid()) {
					tile_data = atlas_source->get_tile_data(cell.get_atlas_coords(), cell.alternative_tile);
				}
			}
			if (tile_data && tile_data->get_terrain_set() == p_terrain_set && tile_data->get_terrain() == p_terrain) {
				connect = true;
			}
		}
		if (connect) {
			cells_with_terrain_center_bit.insert(coords);
		}
	}
	RBSet<TerrainConstraint> constraints;
	
	for (Vector2i coords : p_coords_array) {
		
		TerrainConstraint c = TerrainConstraint(tile_map_node, coords, p_terrain);
		c.set_priority(10);
		constraints.insert(c);
		
		for (int j = 0; j < TileSet::CELL_NEIGHBOR_MAX; j++) {
			TileSet::CellNeighbor bit = TileSet::CellNeighbor(j);
			if (tile_set->is_valid_terrain_peering_bit(p_terrain_set, bit)) {
				c = TerrainConstraint(tile_map_node, coords, bit, p_terrain);
				c.set_priority(10);
				if ((int(bit) % 2) == 0) {