That seems to be a tolerable error but nothing tells you the truth like a test joint. if you have calipers you can measure the variation.
Most shops charge a basic setup fee that makes small jobs expensive. Worth looking into but don't be overly surprised. Of course the setup fee becomes less of a factor on many of the same operations being done with that setup.I might be tempted to live with it, but it might be worth a call to a machine shop to see if they have the tooling to mill it flat. If so I would make my decision based on the cost of the milling.