Tuning is the one area where I think the OEMs have consumers by the balls with respect to warranty. I think any laws favor OEMs with respect to the tunes. Under normal circumstances, yes, they have to prove that the mod led to the failure. That's easy and more clear with suspension lifts, larger tires, power-hungry accessories, etc., but tunes could be added and removed without them knowing. Hence why they added the tracking. And why would they add the tracking if they don't think they could use it against you? They wouldn't. It would be a waste of money and effort.
Don't be fooled, OEMs know that tuners can modify all sorts of parameters that can potentially and very easily damage your engine. And they know that tunes can be removed before service. That's why they implemented the new tracking protocols. I have no doubt that if you get caught with any tune and a powertrain failure that they will blame it on the tune. Knowing that you modified the engine and/or tranny in a way that it was not designed to operate is all the "proof" that they need to void your powertrain warranty. That's the sole reason for adding the tune tracking - warranty protection.
That being said, I would still consider a tune in the future. The main concern right now is with long-term reliability of these new engines and all the TSB/recals that could possibly occur. Give the engines a year or two to see how they last and to let a majority of the problems be worked out. Then if no significant problems, tune away. Or if you don't plan on owning your vehicle for more than a couple of years, tune away. Just do it understanding that there's a very high probablility that your powertrain warranty will be voided in the event of a failure. If that doesn't bother you, then go for it.