The good news is that if you have a CocoaDialog window open, you can still use it after the update is installed, it seems like new UI elements simply can't be created because something is wrong with WindowServer. Existing progressbars can still take in new information (text and bar %), but I don't know if any other CocoaDialog elements have that functionality.
I was already using a progressbar to show "Installing updates, please wait..." so once updates complete I convert that progressbar into an "Updates are complete, restart timer will begin shortly..." and then convert that yet again into a restart timer.
It's a little messy and I am having to redo a good chunk of my script, but it works. My only problem now is capturing policy logs if someone restarts the system early, since the policy hasn't technically finished yet. I used to spin off the restart timer as a new thread with a launchdaemon but I can't do that with this new workflow.
