First things first: After reading your post I looked up the whole deal at the source (Runic) and found an article
they wrote about changing their system, etc. The very last sentence is "Physical retail copies are still fully supported."
Looking at their article about How to update to the latest version
Steam, GOG, Humble Store and PS4 are listed, but physical retail copies are missing.
So there should be a way for you to update your game, but never having purchased Torchlight II, I can't tell you how. Maybe there's an update button in the menu, maybe it's a separate program that's somewhere in the Torchlight II folder. If you can't find it at this point, the best thing to do seems to Contact Runic's Support
Also: I want to say I believe you that they updated the information later than they made the announcement. ( I found that sometimes it's just nice to hear that others don't question every single thing you say... ;) ) GOG really have to work on their timing when making announcements and updating stuff accordingly. I've seen games missing from sales, claiming free games not working in certain regions and festive bugs
that can only be observed on special occasions. But...
There is always something wrong when you're working with something that's constantly updated. The faster the beats, the more likely someone will miss a step. And most of the time stuff gets fixed. I'm not saying you shouldn't blame
them, but you should blame them to their face. Barely a day goes by where I don't write a ticket to support and more than half of the stuff I report on got fixed so far. Some stuff wasn't fixable in time... Other stuff would require redesigning of features. But everything landed on the tables of staff members who can fix it. (And obviously some reports were just me making mistakes.)
I'm sorry for rambling there...
Either way: I hope you find a way to update your game and keep having fun with it. And when you found it you can share it here with us, to help others. ;)
Well the retail game has a launcher for updates, that displays a news Stream, with the current news beeing, that you shall move over to gog or steam as this launcher is no longer supported. In the end it is just the same thing you get at runic, wich they no longer support.