apache certificate list and ssl certificate list

The Apache Cert List is for the internal Apache server to use for GUI client authentication from what I can gather. Here's an example of when you would use this list:

Configuring Remote User Authentication and Authorization

This allows administrators to further control access to BIG-IP via client access certs. The Apache Cert List acts as the client cert list on behalf of the BIG-IP Platform. For your regular client/server SSL profiles you would NOT use this list. But you also make a good point that it's not adequately documented. I'll ask to improve the "Help" section.

-Chase