CGI::App's param() is meant to allow instance scripts to configure the application via the PARAM option to new().

True, but I don't think that it's the only reason for param(). Param was recently a hot topic on the CGI::App mail list. It's also the preferred way for creating your own variables in your subclass of CGI::App without adding to the internal blessed hash directly. As such, you don't always want to do this in new(). It seems to me that the Catalyst stash is performing the same task.