### 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)
Vector<int> data;
	data.resize(pattern.size() * 3);
	int *w = data.ptrw();
	
	int idx = 0;
	for (const KeyValue<Vector2i, TileMapCell> &E : pattern) {
		uint8_t *ptr = (uint8_t *)&w[idx];
		encode_uint16((int16_t)(E.key.x), &ptr[0]);
		encode_uint16((int16_t)(E.key.y), &ptr[2]);
		encode_uint16(E.value.source_id, &ptr[4]);
		encode_uint16(E.value.coord_x, &ptr[6]);
		encode_uint16(E.value.coord_y, &ptr[8]);
		encode_uint16(E.value.alternative_tile, &ptr[10]);
		idx += 3;
	}
	return data;
}
void TileMapPattern::set_cell(const Vector2i &p_coords, int p_source_id, const Vector2i p_atlas_coords, int p_alternative_tile) {