Help! Can't install SSD in my new Mac Mini Server (2012)

Previously I've purcahsed Mac Mini servers and removed one of the two drives, replacing it with an OWC SSD. The hardware change was not hard to do and resulted in incredibly good computers for my employees to use which allowed us to retire several old, slow and abandoned-by-Apple Mac Pros. There were no issues with reformatting the computers after they had SSDs put in.

Today I took delivery of a new Mac Mini server, and started to do the same thing, removing the top HDD and sliding in my SSD, since I have many of them around. Unfortunately, the OS would NOT let me format the disks separately or remove the RAID. The volumes (the original 1 TB that was inside and my 480GB SSD) were both colored red when I booted into Internet Restore mode and ran Disk Util, something I've never seen before, and all it would do was say "there was a problem with your disk, would you like to revert it to a working state?" which in this case means Disk Util forcing my drives back into a RAID whether I want them that way or not. (At one point it fused my SSD and the 1TB drive into a single logical drive that had the correct size but didn't show separate sections, and couldn't be de-RAIDED at all, even when I connected to another computer with the Mac Mini in Firewire target mode.)

I gave up and put a 240 SSD in the lower bay, resulting in a 760GB RAID of two mismatched SSD sizes, which isn't what I wanted but I guess it will do. So far it seems to be working.

My question is, why in the heck is Apple forcing me to run my computers as a RAID and/or not letting me break the system into one hard drive and one RAID, which is what I want? (Having the backup disk right inside the computer is very handy.) Is this some feature to keep us from "making our own" Fusion drives? If Apple is deciding we can't hack or do anything interesting with Mac Minis, this will the last one I purchase, and I'm sure there will be others who do the same.

Since replacing one HDD with an SDD is likely to be the most popular mode imaginable for Mac Minis, can anyone tell me if they got a similar setup to work, and if so what did you do? Can you post the steps here for others who will be in this situation?