Yes the -noGui option prevents ModbusPal from displaying a window, but it still needs to be run from a TTY with the environnement variable DISPLAY set and an Xserver running. This can easily been seen with the following code
unset DISPLAY
java -jar ModbusPal.jar -loadFile=MyConf.xmpp -noGui
So in the end, even though this option promises tio be useful it can't really be used in a Headless environnement