So you have to put every single such file into the configuration.
This is not necessarily the case. I tend to have a single entry point to my mod_perl application (a dispatcher), which handles everything below / except for (eg) paths to static content:
<Location ~ "^/(?!img|stylesheets|scripts|robots.txt|favicon.i
and that single handler parses the request, then hands it off to the relevant handler in my code. Once that handler has processed the request, it passes back the relevant data, template name etc, and my dispatcher handles the template processing and returns the correct response.
This allows you to do pretty much everything in Perl, without having to worry too much about apache.