### 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)
source = *tile_set->get_source(c.source_id);
		if (source->has_tile(c.get_atlas_coords()) && source->has_alternative_tile(c.get_atlas_coords(), c.alternative_tile)) {
			TileSetAtlasSource *atlas_source = Object::cast_to<TileSetAtlasSource>(source);
			if (atlas_source) {
				Vector2i grid_size = atlas_source->get_atlas_grid_size();
				if (!atlas_source->get_runtime_texture().is_valid() || c.get_atlas_coords().x >= grid_size.x || c.get_atlas_coords().y >= grid_size.y) {
					
					Array to_hash;
					to_hash.push_back(c.source_id);
					to_hash.push_back(c.get_atlas_coords());
					to_hash.push_back(c.alternative_tile);
					uint32_t hash = RandomPCG(to_hash.hash()).rand();
					Color color;
					color = color.from_hsv(
							(float)((hash >> 24) & 0xFF) / 256.0,
							Math::lerp(0.5, 1.0, (float)((hash >> 16) & 0xFF) / 256.0),
							Math::lerp(0.5, 1.0, (float)((hash >> 8) & 0xFF) / 256.0),
							0.8);
					
					Transform2D cell_to_quadrant;
					cell_to_quadrant.set_origin(tile_map_node->map_to_local(r_cell_data.coords) - p_quadrant_pos);
					rs->canvas_item_add_set_transform(p_canvas_item, cell_to_quadrant);
					rs->canvas_item_add_circle(p_canvas_item, Vector2(), MIN(tile_set->get_tile_size().x, tile_set->get_tile_size().y) / 4.0, color);
				}
			}
		}
	}
}
#endif 
void TileMapLayer::_physics_update() {