Since Linux has no concept of a base system, it's a stand-alone kernel with a hodgepodge of crap around it - this distinction makes no sense on Linux.
/opt is generally for software distros for which you don't have source; only binaries. Like commercial software packages. More common on Real UNIX(R) because most Linux users outside enterprise aren't running commercial software. You're putting your $500k EDA software under /opt.
"some" is an understatement.
We'll skip PDP-7 UNIX, no hierarchical file system yet.
UNIX v1 on the PDP-11 had an RF11 fixed head disk (1mb) for / and swap, and an RK05 moving head disk (2.5mb) for /usr (the user directories)
By v2 they had added a second RK05 at /sys for things like the kernel, manual pages, and system language stuff like the c compiler and m6.
By v3 they added yet another RK05 at /crp for, well, all sorts of crap (literally), including yacc apparently. /usr/bin is mentioned here for the first time.
I don't feel like looking up when sbin was first introduced but it is not a Bell Labs thing. possibly BSD or AT&T UNIX? Binaries that one would normally not want to run were kept in /etc, which includes thing like init, mount, umount, getty, but also the second pass of the assembler (as2), or helpers like glob. Also i don't know when /home became canonical but at Bell Labs it was never a thing (plan 9 has user directories in /usr where they had always belonged logically).
The lib situation is more difficult. Looks like it started with /usr/lib. By v3 we find the equivalent directory as /lib, where it contains the two passes of the C compiler (no optimization pass back then), C runtime and lib[abc].a (assembler, B, C libraries respectively). /usr/lib had been repurposed for non-object type libraries, think text-preparation and typesetting.
By v4 the system had escaped the labs (see the recent news) and at that point everyone modified the system to their taste anyway. Perhaps it should be noted that the v7 distribution (which is the first that is very clearly the ancestor of every modern UNIX) has no /usr/bin, only /bin. /lib and /usr/lib are split however.
These are just some rough notes and due to a lack of early material they're still not as accurate as i would like. Also UNIX ran on more than one machine even in the early days (the manuals mention the number of installations) so there must have been some variation anyway. Something I'd like to know in particular is when and where RP03 disk drives were used. These are pretty huge in comparison to the cute RK05s.
I once had strange effects on V6 if lib1 and/or lib2 were rebuild by me.
Should be not hard to test.
Are the bugs in the original, or somehow artifacts of how we got it? (Or, phrased differently: Were these bugs present at the University of Utah in 1974, or are they "new"?)
If it turns out to be a timing-related bug it may be that the bug was much less obvious on real hardware.
Otoh it's so much fun to hack and fiddle with the unix kernel :) very zen
Fair point, but I think you misspelled Projective Geometric Algebra