### 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 (Vector2i E_coords : p_painted) {
		TileData *tile_data = nullptr;
		TileMapCell cell = get_cell(E_coords);
		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);
			}
		}
		int terrain = (tile_data && tile_data->get_terrain_set() == p_terrain_set) ? tile_data->get_terrain() : -1;
		if (!p_ignore_empty_terrains || terrain >= 0) {
			constraints.insert(TerrainConstraint(tile_map_node, E_coords, terrain));
		}
	}
	return constraints;
}
void TileMapLayer::set_tile_map(TileMap *p_tile_map) {
	tile_map_node = p_tile_map;
}
void TileMapLayer::set_layer_index_in_tile_map_node(int p_index) {
	if (p_index == layer_index_in_tile_map_node) {
		return;
	}
	layer_index_in_tile_map_node = p_index;
	dirty.flags[DIRTY_FLAGS_LAYER_INDEX_IN_TILE_MAP_NODE] = true;
	tile_map_node->queue_internal_update();
}
Rect2 TileMapLayer::get_rect(bool &r_changed) const {