I add yet another kenv for you to try.
set hint.ahci.nofeatures in /boot/loader.conf or on the boot loader
command line.
I also enhanced the output to indicate which setup command was generating
the CMD TIMEOUT. It should say just after the CMD TIMEOUT stuff.
e.g.
CMD TIMEOUT ...
....
...
...
STS=...
ahcix.x: Unable to set BLAHBLAH
I'd like to know which setup command it was failing on, if it was
failing on one, and whether setting hint.ahci.nofeatures fixes the
problem.
-Matt