When using Multi-JSF feature, some limitations may occur when using non-default implementation. These issues should be documented. I summarized limitations below for those JSF implementations:

Mojarra/MyFaces 2.2.x

Everything should be working according to specification. You may have some problems when trying to call javax.faces.application.ViewHandler constructor, which, although defined is outside of specification. This is caused by removing class JSFLogger.java from EAP. See https://issues.jboss.org/browse/WFLY-3484?page=com.atlassian.jira.plugin.system.issuetabpanels%3Acomment-tabpanel&focusedCommentId=12977141#comment-12977141 for details. If you want to fix these issues add <module name="org.jboss.as.jsf"/> to dependencies in module.xml of respective jsf-injection module.

Mojarra/MyFaces 2.1.x/2.0.x

Please note that the EAP is fully certified Java EE 7 container. After user installs alternative JSF implementation version 2.1 and below, this statement is not applicable anymore. Users should expect that these versions are compliant with JSR-314 so there are a lot of missing features against JSR-344 which specifies JSF 2.2.