They're taking legacy sites and modernising them. They aren't re-writing HMRC's VAT manual and never claimed they were.
You call it identical, but they've altered the underlying HTML layout and change the stylesheet to make it work better in modern browsers and made it easier to interact with using touch devices.
That was their entire spec. That is their job. They've done their job. And while the content is "identical" by design, they fixed the part that was broken: bad markup and poor styling.
PS - The old site looks absolutely terrible in Chrome 40. It "works" but I need to zoom to 200%, and with a touch device I keep hitting the wrong link because they're so close together.