The thing is, you also shouldn't be using apt or whatever for managing project dependencies, unless you and all your fellow devs match Prod exactly, both with distro and exact versions of everything. People do it anyway, but it's bad practice for exactly the same reason that using Brew for it is bad practice, and it's barely easier than doing things right (and, very early in the life of a project, it'll become less easy than doing it right).

It's not about project philosophy, it's about using the right tool for the job. Now, since people keep running into this problem, maybe they ought to put a warning about that right up top in a big banner on the site, I dunno, but it's not specific to Homebrew.

Imo you shouldn't use a typical Linux distro package manager for project dependencies either, unless you're only ever gonna deploy every app you're developing on that machine to the same version of the same distro.

This is not because there's anything really wrong with them for what they're designed to do, but they install packages globally, and different projects may want different versions of the same thing.