Why mention it though? At the time it was formed, the Scottish govt sought advice on the VAT impact of their proposed way of setting up the force, and were told unambiguously by Treasury that the framework (s33 rebate) under which the VAT rebate had existed for regional forces would be lost. So they knew at the outset that creating a single national force would mean the loss of the VAT rebate, and went ahead anyway. Any cries now over this 'unfairness' are political, and also not comparing like for like.
In comparison, different 'national' forces deal with the same issue in different ways. In Northern Ireland they do effectively 'pay' VAT, but through an adjustment to their block grant rather than the method that impacts Police Scotland, even though PSNI get their VAT rebated first through a s99 rebate. All funding through through the Northern Irish Executive is treated as local/regional spend rather than national, which is the differentiator on s33. The National Crime Agency only gets VAT rebated for contracted out services only through a s41 rebate - similar to how other national agencies are treated.
None of that explains the horrendous IT fiascos up north though. Kudos to Police Scotland though for at least getting money back instead of ploughing on regardless.