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I've stumbled upon the solution. I rearranged my SATA connections so the drives use consecutive SATA interfaces. Prior to this, the drives were using SATA interfaces 1, 3, and 5. Now I have them cabled to use 0, 1, and 2. When I reboot now, all the drives are available.

I just built a machine with a GigaByte GA-Z270X-Ultra Gaming mother board using Unibeast, and Multibeast. It has a SSD drive for the boot device, and has two SATA spinning disk HDD drives installed. When I boot from a powered-off state, Disk Utility can see all three drives. However, if I...