Linux has copy-on-write block devices that make it possible to efficiently layer container filesystems. FreeBSD has no such thing as far as I know; the best you can do involves hard links (correct me if I'm wrong).
You are incorrect, FreeBSD has ZFS file system as a first class citizen and that allows all these things (and much more). Check out tools like iocage[1] that are using it in very user friendly manner.
Additionally, a hardlink solution (as you point out) really doesn't sound too outrageous to me. A trivial tool to write to manage immutable things like binaries. Or is there some trouble I'm failing to see (possible)?
You're right. My personal reference for unionfs is NetBSD, which doesn't include such a warning [0]; apparently freebsd's implementation needs some love.
