Only a guess, but it probably does not have to do with the invisible boot partition, which I assume to be the 200 MB EFI system partition ("ESP") partition created on GPT (GUID Partition Table) hard drives by Apple's formatting tools. As
Technical Note TN2166: Secrets of the GPT explains in the "ESP Explained" section, Macs support the ESP, although Apple does not currently use it for anything -- thus, there isn't likely be be anything in it that needs to be updated.
More likely, the message has to do with updating the various boot files mentioned in
System Startup Programming Topics: The Boot Process on the boot volume itself.
As you can see from that topic, the boot process potentially involves several different files, including two copies of the boot.efi boot loader (& possibly another for RAID boot configurations), a pre-linked kernel cache, etc. It is fairly obvious from the description of the various boot options that a less ambiguous message that actually described which files were being updated would be verbose, arcane, & of little value to most users.
In my experience, the message only shows up while the process is running; IOW, when it is checking & potentially updating the boot-related file(s).