You can't do a lot of the configuration that can be done in <Perl> sections after the configuration is parsed (e.g. set the server admin), but you can do things like change handlers (see the push_handler and set_handler methods).

And if you haven't gotten it, I'll reccomend the mod_perl Developer's Cookbook (ISBN 0672322404) for the second time today. It's a good companion to the ORA Eagle book (read that first if you're not familiar with the apache request cycle; then read the cookbook to find out common idioms and best practices).