We have them in here almost daily with the MIL on. I am not sure I'd "panic", but the push to delete/tune it is justified. They went from fragile to, well, something slightly worse.
But you can see how it plays out, and how much the warranty gets called upon (and how well you and your car get treated with it) and see how it goes.
The intake manifold issues we already knew about, and there is an updated unit for that, as well as an aftermarket "band-aid" kind of fix which does work most of the time.
The DPF cracking still happens, only now it happens more often AND they took the low pressure EGR filter tube out for the "fix" so now when it cracks instead of just clogging that filter up and setting an EGR insufficient flow DTC it just sends all the soot right into the inlet side of the turbo... where it gets compressed and slowly builds up a black filth inside the entire charge air tract. Oh, and the DPFs go on national backorder every few months or so.
The intercooler icing is even worse now, too, because this is a direct result of the low pressure EGR operation, and when the fix was applied, it was done to lower NOx... well the only way to lower NOx without adding SCR is to run an even MORE aggressive EGR duty cycle. And they (VoA, dealers) still seem to keep their head in the sand over the cold weather intercooler kit availability (there is a TSB about this).
No change in the rest of the stuff really. Turbochargers fail more often than the older cars, but not as bad as the CKRA in the Passat, and I think with some reasonably smart driving they are not horrible. I've just seen engine harness #2 on one, but that (like the other) were in excess of 250k miles, which isn't anything different than the BRM cars before them (other than a more expensive harness and more labor intensive to replace).
The CJAA does not seem to have the post-fix oddities that the CKRA seems to have, though. I am not sure I would want to depend on one of these every day though. I'd have a backup plan. That sucks to say that, and I am a huge fan of the brand, but....
I will say this though, the cars that get driven a lot... long highway miles, no short trips, tend to be much less problematic. Of course, a delete/tune makes 90% of the issues vanish AND the car runs better (more power) and the fuel economy improves.
FWIW, I would not do anything until you experience it for yourself. You may find it works perfectly just as it is.