It's not mystical at all and if you Google it plenty of people have had warranty refused. Anything you change is detectable if you know where to look but that's IF you know where to look. It's the fact some companies and people say it can't be detected when it actually can.
I also suspect that since Dieselgate, VAG have looked at all areas of the business to see where cost savings can be achieved, and warranty claims will be one such area.
And judging by what I’ve read on various VW forums. VW do seem to be doing more checks now than they used to prior to warranty claims being authorised. With wheels that had succumbed to white worm, the dealer used to just take a photo of the defective wheel to submit for the warranty claim to be authorised. They now measure the thickness of the paint / powdercoat / lacquer to check for signs of refurbishment.
So I’d be surprised if VW don’t also now carry out more thorough checks with powertrain warranty claims for evidence of a tuning box having been fitted to a car, as well as checking to see if a car has been mapped.