ok, the problem seems to be that Steam is executing run_steam.sh which has no parameters passing to script (no $@ or $1). I'm moving discussion to Frictional Games forums:
http://www.frictionalgames.com/forum/thread-19967.html
because this is game related and closing this issue.
Nothing extracted yet.
I tried mod White Nights which requires to add wn_config/main_init.cfg to launch options.
Standard:
Amnesia: The Dark Descent (right click) -> Properties -> Set Launch Options... (and added wn_config/main_init.cfg)
is not working.
However when I launch game manually from command line:
cd ~/.steam/steam/SteamApps/common/Amnesia\ The\ Dark\ Descent
./Launcher.bin64 wn_config/main_init.cfg
it works.