when using cli scripts jboss-cli.sh and jboss-cli.bat and you cannot write in $JBOSS_HOME because it is serving many server instances, you can override default jboss-cli.xml setting -Djboss.cli.config in $JAVA_OPTS but you cannot override logging.configuration because in both scripts is set with default after expanding $JAVA_OPTS

last lines of bat script could be modified as follows:
echo "%JAVA_OPTS%" | findstr /I "logging.configuration" > nul
if errorlevel == 1 (
set "JAVA_OPTS=%JAVA_OPTS% -Dlogging.configuration=file:%JBOSS_HOME%\bin\jboss-cli-logging.properties"
) else (
echo logging.configuration already set in JAVA_OPTS
)

"%JAVA%" %JAVA_OPTS% ^
-jar "%JBOSS_RUNJAR%" ^
-mp "%JBOSS_MODULEPATH%" ^
org.jboss.as.cli ^
%*

Last lines of sh script could be modified as follows:
LOG_CONF=`echo $JAVA_OPTS | $GREP "logging.configuration"`
if [ "x$LOG_CONF" = "x" ]; then
JAVA_OPTS="$JAVA_OPTS -Dlogging.configuration=file:$JBOSS_HOME/bin/jboss-cli-logging.properties"
else
echo "logging.configuration already set in JAVA_OPTS"
fi

1. Sample JPDA settings for remote socket debugging
   #JAVA_OPTS="$JAVA_OPTS -agentlib:jdwp=transport=dt_socket,address=8787,server=y,suspend=n"

eval \"$JAVA\" $JAVA_OPTS -jar \"$JBOSS_HOME/jboss-modules.jar\" -mp \"${JBOSS_MODULEPATH}\" org.jboss.as.cli '"$@"'