Earlier quoted context omitted.
What issues have you experienced due to the merging of those directories?
That would imply that I've drank the Fedora/FDO/systemd Kool-Aid and trashed a perfectly working FHS. I have no interest in wasting the time trying to conform to their nonsense.
(My best thought so far is having multiple hosts sharing a single /usr over NFS while having per-host root filesystems, but I've never actually seen that done. I've also thought about building a distro that kept its initramfs as root and just mounted everything else into it, but that's even further off the beaten path.)