Yeah I believe they did go back to a physical & encrypted EPROM chip on some TSI engines, maybe MK6? MK5 can be flashed as we all know.
Only snag with the MK5 ECU is it records how many times the ECU has been flashed, which afaik, cannot be reset back to 0. I think you need a new ECU from VW in a 'virgin' state if you want to start over.
There's always a certain amount of reverse engineering to be done on these things by aftermarket tuners, so I can understand some getting blown up!!
I think the MK7 Golf R's ECU can be flashed but it throws a "TD1" warranty code. A lot of people leasing a 7 R got caught out with that.