It is kind of a pain to install a second perl alongside the distro's perl installation to keep from breaking things, but I've found it worthwhile for the polish and reliability I get with the management tools for my distro.
I don't think your original post fails at all. I'm a big believer that common wisdom should be used in common situations, but that sometimes it falls down. You just need to be careful about when and how you break the rules and make sure there's actual benefit from it. I can't speak to your case very directly, because I'm not as familiar with your situation as you are. From what you've said, though, you may have one of those situations in which it's worthwhile to write an exception in your local copy of the rules. Just be sure you write it legibly, and, well, cover your behind.