Documentation typically is for running Teiid in JBoss EAP environment. Like above configuration about the logging is JBoss EAP specific. In embedded Teiid, it is up to you where you want channel the log messages. by default they use native java logging modules. If you want you can use "LogManager.setLogger" method to forward they to your favorite logger like Log4J, then use that frameworks configuration to control the logging.
As per buffer manager settings, you can override "protected BufferServiceImpl bufferService" field in EmbeddedServer and add whatever configuration defaults you want.