Where can I find the GOG version of Torchlight 2's save folder under Linux?
Solution 1:
Sorry, with my current reputation I can't add a comment under your question, so if you already did what I will mention now, I will delete this answer.
Did you have a look at this? Someone wanted to transfer his Windows save file(s) to the Linux version and wrote that it worked when he put them into ~/.local/share/Runic Games/Torchlight 2/save/.
If that did not work then according to this post you could look into the ~/.config/unity3d/ folder.
If it is not there either, you could try out a search program, like catfish, and search for the name "save".