You don't need to be flooring the throttle or pulling high revs to be (potentially) doing damage to an engine. As a tuning box can't control timing or fuel, it's just winding up the boost; whenever you're getting more power than you would with the stock program, the ECU's stock programming is making adjustments to compensate, whilst trying to maintain lambda (14.7:1 AFR, or whatever it is at the current temperature/pressure using the current fuel). How effective the ECU is at making adjustments in a very reactionary manner, in response to conditions that it is not expecting, has a bearing on whether the engine can suffer damage. That's my understanding anyway.
A dedicated ECU tune can still maintain safe limits in terms of internal temperatures, knock etc, and still uses all the tools at its disposal like ignition retardation and dumping more fuel into the engine, in order to get those temperatures down and keep the engine safe. A good tune will be no less safe under operating extremes than an OEM tune, and will react in exactly the same way when it detects that a safe threshold has been reached. When the limits haven't been reached, then a tune can advance timing, lean the mixture somewhat and ramp up the boost (all in a coordinated way) to give you more power than the stock tune would - but only until the sensors tell it that it's getting close to sensible limits. (And it's that definition of "sensible limit" that differs between a tuner and VW - VW needs to leave a ton of headroom to allow for drivers who abuse their cars constantly, rev hard from cold, never change the oil or service the car, and worse.)
It could be argued that in some respects an aftermarket tune might even be safer than OEM, if it's been developed to take a more traditional approach to internal temps and run richer than the stock tune would. I don't understand the nuances of how the latest generation EA888 can run so close to lambda all the time, with such high internal temps, and not do damage. I guess a lot of this new strategy is down to economy and emissions - things that are certainly less important to me than the longevity of my engine.
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