You are correct in stating that newconfig does not do an eupdate. However, we
do not think that is the cause of your problem.
When the system is started up, and something "strange" is found (such as a new
card installed), newconfig is run to rebuild the kernel. The file, /newunix,
is used as the base for the new kernel. Since this is a minimal kernel,
modules that you had previously installed will be missing.
It should be possible to write your own script that first called newconfig
and then eupdate to save the new kernel in the Eschatology partition. When the
system finds an invalid kernel and builds a new one, you could then restore
your kernel from Eschatology.
Another method that many people use is to copy /newunix to /newunix.save and
install the modules you want in /newunix. Then, anytime your kernel is rebuilt
from this /newunix, you will automatically have all of the modules you want.