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