As ALIX board user I found this quite annoying as well.
A possible solution is within the boot process to do ntp prior to ntp daemon starts.
A simple script in /etc/init.d with correct link in /etc/rc3.d would allow such time synchronization right after network is up and before ntp daemon starts. Of course certificates get afterwards.
Note that new image is necessary for this to hold as /etc/init.d is in RAM and loaded from the Z iso partition.