In comparison what Audi do when developing a new engine, the testing that aftermarket tuners do is
probably limited. Of course I do not know, so I welcome any tuner to contradict me by revealing how many hours they run tests on a tuned engine on a dyno in an environmental chamber, as an example. So my point is that whilst these tuners do a great job, they are providing a product which is in part sold at the buyer's risk. If you question any of them then I would expect most if not all to advise that since the tune is increasing stresses on engine and transmission (and other components), owners of tuned cars should pay extra attention to care and maintenance. But also as I mentioned, there is the matter of whether or not additional modifications are appropriate.
What
@Chop. states above about releasing potential is indeed true, because indeed most forced induction engines are intentionally restricted by the manufacturer. However there is a balance between performance, economy, emissions, reliability etc. so if an owner take the decision to remove the restriction to increase performance he/she need to understand that it will affect the balance, and the key one I am referring to is reliability. My caution that you quoted refers to the fact that there may be reliability consequences of tuning. I have had tuned cars for over 15 years and over that time spent a lot of time on car forums like this, so I stand by my comment that in general tuned cars tend to have more problems than untuned ones.
Neither my tuned B5 S4 nor my current tuned B8 S5 have given me any major problems. However I did once have an unexplained limp mode on the B5. And I know that there is a risk that the supercharger clutch on my CREC engine could slip. Plus there is the question that affects all B8 s-tronic gearboxed cars and not just mine - will it keep working or will it develop a fault (and if it does, will my tune have contributed?). However the fact that I have not experienced major problems does not make me overconfident because as noted I have read plenty of reports of tuned cars having problems so I shall continue to try to mitigate the risk. I will continue to ensure that my car is properly maintained, with services
in advance of the schedule recommended for an untuned car, and I will continue to pay attention to any signals my car gives that something could be wrong so that I can react to it sooner than later.