### 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)
while (scenes.has(next_scene_id)) {
		next_scene_id = (next_scene_id % 1073741823) + 1; 
	};
}
int TileSetScenesCollectionSource::get_tiles_count() const {
	return 1;
}
Vector2i TileSetScenesCollectionSource::get_tile_id(int p_tile_index) const {
	ERR_FAIL_COND_V(p_tile_index != 0, TileSetSource::INVALID_ATLAS_COORDS);
	return Vector2i();
}
bool TileSetScenesCollectionSource::has_tile(Vector2i p_atlas_coords) const {
	return p_atlas_coords == Vector2i();
}
int TileSetScenesCollectionSource::get_alternative_tiles_count(const Vector2i p_atlas_coords) const {
	return scenes_ids.size();
}
int TileSetScenesCollectionSource::get_alternative_tile_id(const Vector2i p_atlas_coords, int p_index) const {
	ERR_FAIL_COND_V(p_atlas_coords != Vector2i(), TileSetSource::INVALID_TILE_ALTERNATIVE);
	ERR_FAIL_INDEX_V(p_index, scenes_ids.size(), TileSetSource::INVALID_TILE_ALTERNATIVE);
	return scenes_ids[p_index];
}
bool TileSetScenesCollectionSource::has_alternative_tile(const Vector2i p_atlas_coords, int p_alternative_tile) const {