I tried installing via Software Update. The update appeared to succeed, and I proceeded to reboot. After it powered back on, I got the Gigabyte splash screen, and then...nothing! Just a black screen, no Clover. I tried multiple times, and also tried letting it sit in this state for about an hour, but Clover never loaded. I guess the update seemed to have corrupted the Clover install or EFI partition in some way? Has anyone encountered this?
Luckily, I still have my USB installer, so I booted Clover from that. I'm not sure if it was there before, but I think a new "Install from Mojave" partition appeared. I'm not sure if it's related to the update, but I'm not able to boot from that partition, as I get a "couldn't allocate runtime error" which slide=0 doesn't fix (normally I don't have to use this boot flag to boot from "Mojave").
Finally, I reinstalled Clover (upgraded from r5103 to
r5108) to my SSD, rebooted, and ran SecUpd2020-002Mojave.pkg and SecUpd2020-002Mojave.RecoveryHDUpdate.pkg from /Library/Updates/061-90745. Rebooted again, picked my regular "Mojave" partition, and the update seems to have applied. (Thanks to
@UtterDisbelief for the solution on running the individual packages!)
Does anyone know if any of the other packages should also be installed?