standalone.xml should be marked as default configuration in configuration guide and getting started guide. Same for domain.xml. Also other configuration could be used with EAP.

• getting started guide
  • Chapter "2.3. JBoss EAP Management"
• Configuration guide
  • Chapter 3. JBoss EAP Management

Original text:
JBoss EAP uses a simplified configuration, with one configuration file per standalone server or managed domain. Configuration for a standalone server is stored in the EAP_HOME/standalone/configuration/standalone.xml file and configuration for a managed domain is stored in the EAP_HOME/domain/configuration/domain.xml file. Additionally, the configuration for each host controller in a managed domain is stored in the EAP_HOME/domain/configuration/host.xml file.

New text:
JBoss EAP uses a simplified configuration, with one configuration file per standalone server or managed domain. Default configuration for a standalone server is stored in the EAP_HOME/standalone/configuration/standalone.xml file and default configuration for a managed domain is stored in the EAP_HOME/domain/configuration/domain.xml file. Additionally, the configuration for each host controller in a managed domain is stored in the EAP_HOME/domain/configuration/host.xml file.