An option to define paths for the Linux installation would be nice, yes. I always feel like going on a quest when I need to look into my options.cfg, because first I need to find it, inside a hidden file that I always forget (but don't access often enough to warrant a shortcut/link to it).
It's similar for the screens/saves and data, but I access those often enough that now I made links.
If I could, I would lump everything under "/home/username/Documents/OpenXCom/", with a subdirectory for data and another one for saves.
I had some games under Windows that did that, and I really liked the ease of access to their data.