The system and home partitions had been pre-formatted as follows:

# mkfs.nilfs2 /dev/sdc1
# mkfs.nilfs2 /dev/sdc3

I also did a final, quick test. I formatted /dev/sdc1 as ext2 to see if the installer would try to force me to format again, and it did not.

Refracta Installer screenshot 1:

Refracta Installer screenshot 2:

Refracta Installer screenshot 3:

Refracta Installer screenshot 4:

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Refracta Installer screenshot 6:

An idea just came to me about what might have caused this. Originally, I wasn't going to use encryption because this system is basically a test, and I'm not planning to use it for very long. However, when I saw the installer option to encrypt /home, I decided to check it. But now that I'm thinking about it, I'm not sure that this will work for a pre-formatted partition. The way the installer works, doesn't formatting the partition need to come after the encryption?