Ok, this is a bit confusing and has been happening for at least the last 5 macOS updates I've done (both public beta and full releases in Sierra). Here's what happens:
I go to the App Store and tell the computer to install the update from the updates tab. The computer gives me the 60-second restart warning, I quit app store and manually hit the restart button on that notification. The computer begins installing the update. To this point the process is normal. Here's where it gets weird.
The update never finishes installing. For example, on updating to 10.12.5 beta 3 (from beta 2), it was stuck with the loading bar at 16 minutes left for about an hour. I resolved this problem simply by holding down the power button for 10 seconds to force a shutdown. Then I pressed the power button again to turn the computer on. Not only does the computer turn on, it has also successfully installed the update. This has happened at least five times. It always appears on the screen that the update has frozen, but it seems that the update completes successfully, but fails to tell the computer to reboot.
A new twist on this occurred last night. I went straight from 10.12.5 beta 3 to 10.12.6 beta 3 (I'm generally better about updates, but I needed to have the computer running without shutdown for 42 days). Yesterday night I followed the same procedure I outlined in the second paragraph. Instead of showing the loading bar, the screen went to computer black (black screen, but backlight still on). That's the same state I discovered in this morning, 7 hours later. I did the trusty force restart, and now am successfully running 10.12.6 beta 3.
My question is two-fold: What could be causing this to be happening, and how can I get my computer to update normally? While the manual reboot step doesn't bother me, I am afraid that one day an update will fail, and as it takes ~12 hours for this computer to restore from one of my backups, it is something I would rather not have to deal with.