One of the most obvious things that broke booting with a seperate /usr
is not GNOMEs fault, but GRUB 2's fault.
the move of /bin to /usr/bin (for things like cp,mv,ln,ls) came after
the breakage of /usr, but is symptomatic of some distros cavalier
attitudes to the problem.
/usr/lib/udev.....
/usr/lib/systemd.....
were both placed in /usr despite objections from a number of folks.
So claims that udev and systemd are not responsible are not true.
/usr/lib/e2initrd-helper was placed in /usr despite objections.
/usr/lib/libdevmapper* was moved despite objections...
/usr/lib/liblvm2* helpers were placed in /usr despite objections...
There were deliberate placements of "new" or updated libraries in /usr
that were known ahead of time that would break the use of a separate
/usr filesystem.
It was pointed out quite plainly at the time, and the placements were
made anyway, dismissing the concerns are "mere historical artifacts" or
"clinging to ancient and outmoded traditions."
The *same things* are still being cited (about being outmoded) in
dismissing concers about forcing useres to adopt technologies they do
not want to use.