Ok wrong guess ! Thanks for your inquiry by the way
As far as I understand boot sequence (no so much), the reboot happens just before kernel :
Clover (preboot.log) > boot.efi (influenced by OsxAptioFixDrv.efi, no log but seems OK as we have no error and the "++++++" > kernel (log in console)
The reboot happens just after the "+++++++" without any message in verbose, that's why I though of a kernel problem, but now it has been checked.
I tried boot.efi from 10.11.6 Combo without luck.
I tried to look at the sources to understand what happens at this moment but I didn't find anything as I don't understand much (I'm a user not a dev...)
I don't know how to debug this as preboot .log seems OK and I have no log in console.
Another question : do you remember if this security update operates in two times, I mean one before reboot and one after reboot ? Because if so, I never manage to get the second stage to load ... which could explain the reboot.
EDIT : do you think I should add debug=yes in the KernelAndKextPatches section of my config.plist and see what happens ? Or is it useless ? (I can't test right now, I'm away from my hack for several days ... )