Hello!
Seems like ./build phpmyadmin is not using the custom config in ${CWD}/custom/phpmyadmin/config.inc.php.
if [ "${PMA_CUSTOM_CONFIG}" != "" ] && [ -e ${PMA_CUSTOM_CONFIG} ]; then
echo "Installing custom PhpMyAdmin Config: ${PMA_CONFIG}"
cp -f ${PMA_CONFIG} ${REALPATH}/config.inc.php...