Ok, now I'm confused. In your OP, you said:

However, only the latter works with CGI::Application::Plugin::AutoRunmode

which implies to me that something, well, isn't working when you don't "use base ...". I'm curious as to what it is that isn't working when you "use CGI::Application::Plugin::AutoRunmode; push @INC, qw(CGI::Application::Plugin::AutoRunmode);" - what the symptoms are, etc., that "use base qw(CGI::Application::Plugin::AutoRunmode);" fixes?