Sigh ... gobolinux solved this quite elegantly over 20 years ago, and to this day most folks don't quite grok how simple and elegant their solution was.
> /bin is a link to /System/Index/bin. And as a matter of fact, so is /usr/bin. And /usr/sbin
So, they're doing exactly the same thing as Debian is doing on the default merged configuration ?
Issues seen on Debian are not the system using symlinks or not, but packages failing when exchanged between system that still had both /bin/ and /usr/bin as separate directories, as it was historically, and the new merged systems. Gobolinux being a from scratch built distro with no transition history, I am not sure how it can be seen as a better example here.