I know it's a little late now, but THIS is what having an external, fully-bootable backup drive is all about...
Doesn't solve this problem.
I've re-installed 10.12.6 3 times now. It doesn't matter if I boot from external or internal. After installing SU2017-001, the mac is stuck at boot. Meaning, if I don't make a clean install and manually move my own data, I can't install security updates anymore. I have a ticket in applecare, but they are slow and I've got some wrong advice so far.
I'd just like to know how to investigate
what really hangs the booting...
EDIT: I did a clean install on external drive and SU went fine with it. But I don't have big enough spare drive to clone my whole internal FD or timemachineBU to it. Something in my internal FD's system hangs the mini at boot after SU and I would just like to know what...