### 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_V(!pattern.has(p_coords), TileSet::INVALID_SOURCE);
	return pattern[p_coords].source_id;
}
Vector2i TileMapPattern::get_cell_atlas_coords(const Vector2i &p_coords) const {
	ERR_FAIL_COND_V(!pattern.has(p_coords), TileSetSource::INVALID_ATLAS_COORDS);
	return pattern[p_coords].get_atlas_coords();
}
int TileMapPattern::get_cell_alternative_tile(const Vector2i &p_coords) const {
	ERR_FAIL_COND_V(!pattern.has(p_coords), TileSetSource::INVALID_TILE_ALTERNATIVE);
	return pattern[p_coords].alternative_tile;
}
TypedArray<Vector2i> TileMapPattern::get_used_cells() const {
	
	TypedArray<Vector2i> a;
	a.resize(pattern.size());
	int i = 0;
	for (const KeyValue<Vector2i, TileMapCell> &E : pattern) {
		Vector2i p(E.key.x, E.key.y);
		a[i++] = p;
	}
	return a;
}
Size2i TileMapPattern::get_size() const {
	return size;
}
void TileMapPattern::set_size(const Size2i &p_size) {