Made DIY fusion drive.... now recovery partition won't boot
Well, I was able to "solve" this in a round-about way.

I used the recovery disk assistant with my MacBook Air to make a recovery SD card. With that plugged into my mini, I was able to successfully boot into it and the disk utility there was able to comprehend my fusion drive.

That done, I then checked and saw that the recovery partition on the SD card was the same size as the recovery partition that wasn't working right, so I did a dd from the SD card overwriting the recovery partition.

The result: my option menu now offers the choice of the fusion drive (booting normally) or the recovery partition, and both work.

What I think may have been going on is that core storage seems to want to turn the recovery partition into a 'boot helper' on encrypted volumes. Perhaps it was trying to do the same thing on this machine, despite the fact that there was a separate boot partition intended to serve that purpose.

I'm not going to mark this as "solved," however, because I think there has to have been a better way.