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Your points are good, but I think you're focusing on the idea of "one module is the application" related to CGI::Application too much.
The way I use CGI::Application is I write a central module, "SuperClass.pm" that has shared functions for all my other modules that make up an entire web application. I then use this SuperClass in all my application modules.
Here's an application module, UserManager.pm, which inherits many of it's functions from SuperClass.:
I then build all my other application modules split logically into appropriately named .pms', but all still sharing the same core. e.g. there's a UserManager.pm, Survey.pm, RSS.pm, Search.pm, etc.
I don't think of developing with CGI::Application like I need to stuff everything into one module at all, put your shared functions into a "SuperClass" and then use that as the API that you develop the rest of your application modules around.
Though I'm pretty much a "lone-wolfer," this methodology seems to lend itself very nicely to working with a team: You articulate to them what is provided by SuperClass, and they code around it. If you need to figure out what someone wrote, you just look at their run modes and you can very easily figure out what's happening. Seems pretty scalable to me.
Hope this helps! I really suggest that anyone looking to make webapps look closely at CGI::Application. It enforces good coding standards, uses the excellent HTML::Template module to great effect, and is very flexible and lightweight.