sqoop-env-template.sh
is a template, meaning it doesn't by itself get sourced by the configurator. If you want it to have a custom conf and load it, make a copy as $SQOOP_HOME/conf/sqoop-env.sh
.
Note: here is the relevant excerpt from bin/configure-sqoop
for version 1.4.4:
SQOOP_CONF_DIR=${SQOOP_CONF_DIR:-${SQOOP_HOME}/conf}
if [ -f "${SQOOP_CONF_DIR}/sqoop-env.sh" ]; then
. "${SQOOP_CONF_DIR}/sqoop-env.sh"
fi