I'm not able to configure AS7 to use all configuration files from different location than standard $JBOSS_HOME/standalone/configuration or $JBOSS_HOME/domain/configuration. I'm using system properties described on confluence [1]. The same for log files.

AS7 always requires logging.properties from $JBOSS_HOME and it writes boot.log into directories under $JBOSS_HOME depending whether standalone or domain is running.

The root of this problem is in scripts:
standalone.sh/.bat

-Dorg.jboss.boot.log.file=$JBOSS_HOME/standalone/log/boot.log
-Dlogging.configuration=file:$JBOSS_HOME/standalone/configuration/logging.properties

domain.sh/.bat

-Dorg.jboss.boot.log.file=$JBOSS_HOME/domain/log/process-controller/boot.log
-Dlogging.configuration=file:$JBOSS_HOME/domain/configuration/logging.properties

-Dorg.jboss.boot.log.file=$JBOSS_HOME/domain/log/host-controller/boot.log
-Dlogging.configuration=file:$JBOSS_HOME/domain/configuration/logging.properties

My idea:
Introduce LOG_PATH + CONFIGURATION_PATH properties (similar to MODULEPATH property) in .sh/.bat files to have logs and configuration outside AS7/EAP6.

Default LOG_PATH by default would be $JBOSS_HOME/domain/log or $JBOSS_HOME/standalone/log.
Default CONFIGURATION_PATH would be $JBOSS_HOME/domain/configuration or $JBOSS_HOME/standalone/configuration.

Definitions of -Dorg.jboss.boot.log.file= and -Dlogging.configuration= would be changed to use LOG_PATH + CONFIGURATION_PATH properties.

Changes for server instances can be modified using system properties – jboss.server.log.dir + jboss.server.config.dir OR jboss.domain.log.dir + jboss.domain.config.dir + jboss.domain.servers.dir.

[1] https://docs.jboss.org/author/display/AS71/Command+line+parameters