If you make your own linux distro from scratch, you can get many of the open source pieces of a linux distro to use whatever layout you want, while some pieces do require patching and fixing ... but you do have the source :)
The problem with Gobo is that this progression never works:
New FS Layout -> User Adoption -> Profit
Because at the end of the day the layout of the filesystem is never the selling point on any given distro. It always comes down to the software - either the amount of it, or the newness of it, and that is why people flock to Ubuntu and Arch respectively.
It is much more prudent to argue for filesystem improvements in those distros, and get them implemented there, than to fork it out. Gobo demonstrated both the validity and the utility of the approach, but it is up to distro makers to actually use the evidence given that the traditional Unix layout is garbage.
Much like Gobolinux, Guix also has a completely different filesystem layout. Packages are installed into their own namespace under /gnu/store but then linked to expected locations under a profile root (such as ~/.guix-profile).
That's the one I was trying to think of! Yeah, they solved the directory problem. NixOS solved the packaging problem. Little projects doing what they can to fix the UNIX/Linux mess.
archlinux has for a couple of years symlinked /bin, /sbin, and /usr/sbin to /usr/bin, and /lib, /lib64 to /usr/lib https://wiki.archlinux.org/index.php/arch_filesystem_hierarc...
If you make your own linux distro from scratch, you can get many of the open source pieces of a linux distro to use whatever layout you want, while some pieces do require patching and fixing ... but you do have the source :)