The only way its going to happen is if jira issues are raised which illustrate the usecases that are failing. To date any issue you have raised has been resolved as far as I know.
Before I log a jira issue (just in case I've done something wrong), I am experiencing a similar issue with JBoss 4.0.2, log4j 1.2.9 and hibernate 2.1.8
Although the logs show that JBoss is loading my log4j jar properly (I have specified isolated classloading using jboss-web.xml with java2ParentDelegation set to false) and all my other logging is going to my app log file correctly, hibernate log entries still go to server.log as per the log4j.xml in the standard config.
I can only guess that this is because hibernate is not being loaded by my hierarchical classloader, however I can't find the hibernate jars anywhere else in my standard install (apart from the deployment war which I have removed for the moment).
So, it seems to me that the issues referred to in the initial post are at least still present in 4.0.2. Of course it's altogether possible that I've missed something out as I'm relatively new to JBoss and information on this topic isn't exactly abundant...
Please let me know if I should go ahead and log a jira issue.