Simply put: All directory names under Addons need to be lowercase! Otherwise, you will likely not see the mods used.
This took me quite a while to discover. Since Windows is not case-sensitive in reference to filenames, but Linux is, this does make a difference.
Otherwise, the game actually runs quite a bit smoother (on average) under Linux, even if you can't use F1 to switch on FPS display (haven't tried F12, but expect it won't work either).