The list below is from the variable used in the server.xml file to the user configuration element.
The user configuration elements can come from the sys1.parmlib concatenation member(IZUPRMCPxx) or in the /var/zosmf/configuration/local_override.cfg file. For example my local_override.cfg file has
KEYRING_OWNER_USERID=START1 KEYRING_NAME=KEY2 KEYRING_TYPE=JCERACFKS
This is so the server uses the keyring START1/KEY2 as the keystore and the trust store.
What values are used?
You can see what values are used by looking in the /var/zosmf/configuration/servers/zosmfServer/bootstrap.properties file. Any changes you make to this file are ignored as the file gets rebuild whenever you start the server.
List of variables
com.ibm.ws.logging.max.file.size=${LIBERTY_TRACE_FILE_SIZE}]
com.ibm.ws.logging.trace.append=${LIBERTY_TRACE_FILE_APPEND}]
com.ibm.ws.logging.trace.file.name=${LIBERTY_TRACE_FILE}]
com.ibm.ws.logging.trace.max.files=${LIBERTY_TRACE_FILE_NUM}]
com.ibm.ws.logging.trace.specification=${LOGGING}]
com.ibm.ws.tcpchannel.useZosAio=${LIBERTY_USEZOSAIO}]
com.ibm.ws.zos.core.angelName=${IZU_ANGEL_NAME}]
izu.apps.listener.list=${IZU_APPLICATIONS_COLLECTIVE}]
izu_apps_listener_waittime=${IZU_APPLICATIONS_LISTENER_WAITTIME}]
izu.authCache.timeout=${AUTHCACHE_EXPIRE}m]
izu.ciphers.list=${IZU_CIPHERS_LIST}]
izu.data.dir=${IZU_DATA_DIR}]
izu.dmap.mem.size.in.entries=${LIBERTY_DYNCACHE_SIZE}]
izu.hostname=${IZU_APPSERVER_HOSTNAME}]
izu.http.logging.logformat=${ACCESS_LOG_FORMAT}]
izu.http.logging.maxfiles=${ACCESS_LOG_FILES}]
izu.http.logging.maxfilesize=${ACCESS_LOG_SIZE}]
izu.http.logging.switch=${ACCESS_LOG}]
izu.http.options.removeserverheader=${LIBERTY_REMOVE_HEADER}]
izu.http.port=${IZU_HTTP_PORT}]
izu.https.port=${IZU_HTTP_SSL_PORT}]
izu.http.wlm.classification.resource=${DEFAULT_WLM_RESOURCE}]
izu.http.wlm.transaction.class=${DEFAULT_WLM_CLASS}]
izu.install.dir=${IZU_INSTALL_DIR}]
izu.javaclasses.lib.dir=${JAVA_CLASSES}]
izu.listenBacklog=${LISTEN_BACKLOG}]
izu.long.concurrent.jndi=${LONGWORK_JNDI_NAME}]
izu.long.transaction.class=${LONGWORK_WLM_CLASS}]
izu.long.wlm.context.option=${LONGWORK_CONTEXT_OPT}]
izu.ltpa.expiration=${LTPA_EXPIRE}m]
izu.ltpa.key.file.name=${LTPA_FILE}]
izu.ltpa.key.password=${LTPA_PASS}]
izu.profile.prefix=${IZU_SAF_PROFILE_PREFIX}]
izu.scheduled.concurrent.jndi=${SCHEDULED_JNDI_NAME}]
izu.session.timeout=${SESSION_EXPIRE}]
izu.shared.library=${SHARED_LIB_NAME}]
izu.spi.kernel.service.lib=${LIBERTY_KERNEL_SERVICE}]
izu.spi.logging.lib=${LIBERTY_LOGGING}]
izu.spi.passwordutil.lib=${LIBERTY_PASSWORDUTIL}]
izu.ssl.client.auth.supported=${SSL_CLIENT_AUTH}]
izu.ssl.config=${IZU_SSL_CONFIG}]
izu.ssl.key.store.owner.userid=${KEYRING_OWNER_USERID}]
izu.ssl.key.store.password=${KEYSTORE_PASS}]
izu.ssl.key.store.saf.keyring=${KEYRING_NAME}]
izu.ssl.key.store.type=${KEYRING_TYPE}]
izu.ssl.Protocol=${IZU_SSL_PROTOCOL}]
izu.sso.domain.names=${SSO_DOMAIN_NAMES}]
izu.sso.usedomainfromurl=${SSO_DOMAIN_URL}]
izu.unauthenticated.user=${IZU_UNAUTHENTICATED_NAME}]
izu.user.registry.realm=${USER_REALM}]
izu.usr.lib.dir=${USERLIB_DIR}]
izu.wbem.root=${PEGASUS_HOME}]
izu.zoslogging.msgid=${IZU_ZOSLOGGING_MSGID}]