### 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)
TypedArray<Vector2i> a;
	for (const KeyValue<Vector2i, CellData> &E : tile_map) {
		const TileMapCell &c = E.value.cell;
		if (c.source_id == TileSet::INVALID_SOURCE) {
			continue;
		}
		a.push_back(E.key);
	}
	return a;
}
TypedArray<Vector2i> TileMapLayer::get_used_cells_by_id(int p_source_id, const Vector2i p_atlas_coords, int p_alternative_tile) const {
	
	TypedArray<Vector2i> a;
	for (const KeyValue<Vector2i, CellData> &E : tile_map) {
		const TileMapCell &c = E.value.cell;
		if (c.source_id == TileSet::INVALID_SOURCE) {
			continue;
		}
		if ((p_source_id == TileSet::INVALID_SOURCE || p_source_id == c.source_id) &&
				(p_atlas_coords == TileSetSource::INVALID_ATLAS_COORDS || p_atlas_coords == c.get_atlas_coords()) &&
				(p_alternative_tile == TileSetSource::INVALID_TILE_ALTERNATIVE || p_alternative_tile == c.alternative_tile)) {
			a.push_back(E.key);
		}
	}
	return a;
}
Rect2i TileMapLayer::get_used_rect() const {