Ublue revolves around Flatpaks, and most CLI applications aren't available as a Flatpak. Homebrew contains thousands of CLI packages and libraries, and it works effectively in userspace on atomic/immutable systems, making it the perfect pair
My 2 cents is it would fall on fedora and brew to sort it out. We don't do anything special.
But I think it is more on brew to fix. If home is a symlink then follow the link to the absolute path (or just assume atomic and look in /var/home) Not rocket science
I'm not too keen on including brew on the main image. It goes against the idea of them being unopinionated and not veering too far from upstream.
Instead, I'd be happier removing some of those tools, and moving them downstream (either as RPM or Brew), though it's not as easy to do now they are already on the image