During embedded server startup some properties are set if they're not yet present, however the logic for establishing some of them is different from normal mode.

On normal startup if the jboss.server.data.dir is present 'jboss.server.content.dir' property would be set to ${jboss.server.data.dir}/content [1]. In embedded scenario it is instead set to ${jboss.server.base.dir}/standalone/data/content [2].

[1] https://github.com/wildfly/wildfly-core/blob/master/server/src/main/java/org/jboss/as/server/ServerEnvironment.java#L467-L475
[2] https://github.com/wildfly/wildfly-core/blob/master/embedded/src/main/java/org/wildfly/core/embedded/StandaloneSystemPropertyContext.java#L52-L57