In the UK paper books are zero rated (0%) for VAT so that's not what's going on.
Since the Guardian's writer hasn't heard of the MFN "no ebook underselling" terms of Amazon they probably know still less about the esoterics of VAT. Note that since the publishers are UK based they might have to charge 20% at some point.
However, since all this suggests the publishers can get better terms by going indie and taking the KDP T&C, why don't they do just that ? Because it's NOT TRUE perhaps.