Yes, command line is affected by those settings as well.
Up until v1.3, using -s to view or alter settings would do the requested operation and quit back to command line. I have just pushed a change to the development build that allows using -s:switch=true/false to change settings and proceed to the IDE in case a file is specified in the command line or to proceed with compilation if -x, -c or -z are passed, so there's that now.