### 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)
struct Count {
		int count = 0;
		float probability = 0.0;
		Ref<Texture2D> texture;
		Rect2i region;
	};
	Vector<Vector<Ref<Texture2D>>> output;
	LocalVector<LocalVector<Count>> counts;
	output.resize(get_terrain_sets_count());
	counts.resize(get_terrain_sets_count());
	for (int terrain_set = 0; terrain_set < get_terrain_sets_count(); terrain_set++) {
		output.write[terrain_set].resize(get_terrains_count(terrain_set));
		counts[terrain_set].resize(get_terrains_count(terrain_set));
	}
	for (int source_index = 0; source_index < get_source_count(); source_index++) {
		int source_id = get_source_id(source_index);
		Ref<TileSetSource> source = get_source(source_id);
		Ref<TileSetAtlasSource> atlas_source = source;
		if (atlas_source.is_valid()) {
			for (int tile_index = 0; tile_index < source->get_tiles_count(); tile_index++) {
				Vector2i tile_id = source->get_tile_id(tile_index);
				for (int alternative_index = 0; alternative_index < source->get_alternative_tiles_count(tile_id); alternative_index++) {
					int alternative_id = source->get_alternative_tile_id(tile_id, alternative_index);
					TileData *tile_data = atlas_source->get_tile_data(tile_id, alternative_id);
					int terrain_set = tile_data->get_terrain_set();
					if (terrain_set >= 0) {
						ERR_FAIL_INDEX_V(terrain_set, get_terrain_sets_count(), Vector<Vector<Ref<Texture2D>>>());
						LocalVector<int> bit_counts;
						bit_counts.resize(get_terrains_count(terrain_set));