I've tried to slightly reduce the size of my "MacintoshHD" partition by 256MB, no luck. I've tried using the terminal to remove the EFI partition, because in my setup it shows as "Microsoft Basic" of some kind, which should actually be EFI. No luck due to "Resource busy".
In the end, at the top left in the Apple command, you can select the "disk" to use to restart the system. Select your regular, trustworthy MacintoshHD there and you're back into your regular EFI startup screen, where you can select either Apple or Ubuntu.
Some things are seriously wrong in the update process and I'm not sure I want to use the current software to do my updates. I'm going to try to write a report about this experience to see if Apple can redo some of this process or "auto-fix" some of the issues. I don't have anything valuable in the Ubuntu partitions that I care about (it's re-creatable in 1.5 hours or so), but the Apple philosophy is that things should just "work", and they don't without a proper indication of what failed.
So yeah... not a standard Apple as it's a dual-boot, but certainly using their hardware and some of the indications could be a bit more informative as to why things failed.