### 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)
} else if (components.size() >= 3 && components[1].begins_with("animation_frame_") && components[1].trim_prefix("animation_frame_").is_valid_int()) {
					int frame = components[1].trim_prefix("animation_frame_").to_int();
					if (frame < 0 || frame >= get_tile_animation_frames_count(coords)) {
						return false;
					}
					if (components[2] == "duration") {
						r_ret = get_tile_animation_frame_duration(coords, frame);
						return true;
					}
					return false;
				} else if (components[1].is_valid_int()) {
					int alternative_id = components[1].to_int();
					if (alternative_id != TileSetSource::INVALID_TILE_ALTERNATIVE && tiles[coords].alternatives.has(alternative_id)) {
						if (components.size() >= 3) {
							bool valid;
							r_ret = tiles[coords].alternatives[alternative_id]->get(components[2], &valid);
							return valid;
						} else {
							
							r_ret = alternative_id;
							return true;
						}
					}
				}
			}
		}
	}
	return false;
}
void TileSetAtlasSource::_get_property_list(List<PropertyInfo> *p_list) const {