I know, but that doesn't necessarily make it a good solution.
I've been a sys admin for several large unix systems and variations on the problem Zed describes needed to be hacked around on each and every one of them.
I think we agree. If I were doing an OS now, I'd also ignore the FHS completely, but more to the point: I wouldn't use anything that remotely resembles it either.
/ would have one dir:
/myos
And all OS components are under there:
/myos/bin/python
People can install anything they want outside /myos, but I'd make it very clear that the OS owns this folder and it should not be modified.
I did a little work on this a while back - an LFS system is a good place to start. I was a little ambitious though - I wanted a pure C/python system with no shells (at all - just ipython) and no command scraping - just enough to start SSH and nginx.
It's a lot of work - I think I ended up trying to write an iproute2 replacement using ctypes and quit. I wonder if anyone else would be interested...