This Upper Tier decision indicates that the taxpayer may only claim for an adjustment of VAT overpaid under VAT Act 1994, and not via common law. So you cannot sue HMRC for overpaid or overdeclared VAT. It said that s80(7) has this effect.
But there may be other options for making a claim against HMRC, depending on the particular facts. If your overpayment is due to an HMRC error or misdirection I opine that you can make a civil claim.
This case also discusses the way set-off rules work with the 4-year time limit for making adjustments. But it is complicated by other case law. Unfortunately, for Rank, the time limits worked against the taxpayer, meaning a claim for £67m was lost.