The short answer is that you can't. The reboot is an integral part of the secured BIOS installation process. Nothing can run between the BIOS being placed in memory and the reboot taking place. Your choices are to run the BIOS update as the last step in the customization process or craft the customization script so that it can continue across reboots. If you are running the update process from a separate flash stick using DOS, this is fairly easy to do. Just have a particular step in the overall process create a file on the flash stick to indicate that the step was completed and then have the script check for this file existing and skip forward to the appropriate place in the overall sequence. This is a standard state machine process if you have any experience with them. If you would like some help doing this, just let me know via private email. I am retired from Intel but still willing to help...
Thank you, Scott.
We managed to let it work by just rebooting, updating the bios, then re-imaging the machine again. So essentially our image process breaks during the bios reboot, but then we image it a second time fully. An unfortunate work-around. But thank you for the very helpful information. You at least saved me some time from trying to find a way around the forced reboot.