No, there isn't. You are correct about the IRS identifying the mismatch. Perhaps the best option here is to get your employer to issue you an amended W-2. It is not clear why your employer would sell to cover--as they are required to do--and presumably remit that withholding amount to the federal/state taxing authorities, and yet not include the withholding on your W-2.
You are also correct in that if you add the withholding amount to your cost basis you are only further complicating your tax situation. Given these facts, your best option is to get your employer to issue an amended W-2.
@alexmarin
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