I believe if you're going the Homebrew route you're accepting the cask's versions of things as a means to synchronize installations. This could be handle for teams that need to be using the same versions of specific libraries or apps, system administrators who want to manage upgrades paths, etc.

It could also be as simple as "that's the way it works because that's how homebrew works". It's all symlinks, and I personally am a fan because if I want to cleanup what's been done with Homebrew it's very easy.

I do completely understand your point, and agree to a certain extent, but I'm sure there are situations where you wouldn't want things simply copied and left to run/update on their own.