The VWR warranty is a top up warranty, additional to the normal manufacturers warranty. That is, what VW won't cover because of the mods, the top-up will. Whilst the brochure is written in VW font/print style, and its available on dealers desks, VW UK nor Gormany are rubber stamping the upgrades.
Some Skoda dealers sell Tunit boxes, but they are not approved by VAG either.