### 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)
ERR_FAIL_COND_V_MSG(!tiles.has(p_atlas_coords), false, vformat("The TileSetAtlasSource atlas has no tile at %s.", String(p_atlas_coords)));
	return tiles[p_atlas_coords].alternatives.has(alternative_no_transform(p_alternative_tile));
}
int TileSetAtlasSource::get_next_alternative_tile_id(const Vector2i p_atlas_coords) const {
	ERR_FAIL_COND_V_MSG(!tiles.has(p_atlas_coords), TileSetSource::INVALID_TILE_ALTERNATIVE, vformat("The TileSetAtlasSource atlas has no tile at %s.", String(p_atlas_coords)));
	return tiles[p_atlas_coords].next_alternative_id;
}
int TileSetAtlasSource::get_alternative_tiles_count(const Vector2i p_atlas_coords) const {
	ERR_FAIL_COND_V_MSG(!tiles.has(p_atlas_coords), -1, vformat("The TileSetAtlasSource atlas has no tile at %s.", String(p_atlas_coords)));
	return tiles[p_atlas_coords].alternatives_ids.size();
}
int TileSetAtlasSource::get_alternative_tile_id(const Vector2i p_atlas_coords, int p_index) const {
	ERR_FAIL_COND_V_MSG(!tiles.has(p_atlas_coords), TileSetSource::INVALID_TILE_ALTERNATIVE, vformat("The TileSetAtlasSource atlas has no tile at %s.", String(p_atlas_coords)));
	p_index = alternative_no_transform(p_index);
	ERR_FAIL_INDEX_V(p_index, tiles[p_atlas_coords].alternatives_ids.size(), TileSetSource::INVALID_TILE_ALTERNATIVE);
	return tiles[p_atlas_coords].alternatives_ids[p_index];
}
TileData *TileSetAtlasSource::get_tile_data(const Vector2i p_atlas_coords, int p_alternative_tile) const {
	ERR_FAIL_COND_V_MSG(!tiles.has(p_atlas_coords), nullptr, vformat("The TileSetAtlasSource atlas has no tile at %s.", String(p_atlas_coords)));
	p_alternative_tile = alternative_no_transform(p_alternative_tile);
	ERR_FAIL_COND_V_MSG(!tiles[p_atlas_coords].alternatives.has(p_alternative_tile), nullptr, vformat("TileSetAtlasSource has no alternative with id %d for tile coords %s.", p_alternative_tile, String(p_atlas_coords)));
	return tiles[p_atlas_coords].alternatives[p_alternative_tile];
}
void TileSetAtlasSource::_bind_methods() {