I think it's common sense...
Stick to a reputable tuner and don't go chasing every last BHP and you are likely to be fine.
If people want to wait 3 years to play with their car, fine...personally I'll be bored by then...so I wouldn't hesitate in re-mapping from new or nearly new.
Past experience is enough for me to be happy to do so.
Of course, if you chase every last BHP and have the non-standard inlet/exhaust...then it becomes more obvious...
If you want a re-map then you want more power...that's obvious. If you are prepared to re-map whilst under warranty...then you know the risks.
Personally, if you take the risk, you'd be as well looking at the chance of an engine granade as an opportunity to tune further. How many people are likely to blow up their 2.0 TSI and replace with stock engine/turbo, at their cost?
Avoid the dealer network, and have uprated internals/turbo fitted for about the same cash...and get even more power.
It's a slippery slope...
You pay your money and make your choice.