### 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)
ERR_FAIL_COND(p_atlas_coords.x < 0 || p_atlas_coords.y < 0);
	ERR_FAIL_COND(p_size.x <= 0 || p_size.y <= 0);
	bool room_for_tile = has_room_for_tile(p_atlas_coords, p_size, 1, Vector2i(), 1);
	ERR_FAIL_COND_MSG(!room_for_tile, "Cannot create tile. The tile is outside the texture or tiles are already present in the space the tile would cover.");
	
	TileAlternativesData tad;
	tad.size_in_atlas = p_size;
	tad.animation_frames_durations.push_back(1.0);
	tad.alternatives[0] = memnew(TileData);
	tad.alternatives[0]->set_tile_set(tile_set);
	tad.alternatives[0]->set_allow_transform(false);
	tad.alternatives[0]->connect("changed", callable_mp((Resource *)this, &TileSetAtlasSource::emit_changed));
	tad.alternatives[0]->notify_property_list_changed();
	tad.alternatives_ids.push_back(0);
	
	tiles.insert(p_atlas_coords, tad);
	tiles_ids.push_back(p_atlas_coords);
	tiles_ids.sort();
	_create_coords_mapping_cache(p_atlas_coords);
	_queue_update_padded_texture();
	emit_signal(SNAME("changed"));
}
void TileSetAtlasSource::remove_tile(Vector2i p_atlas_coords) {