One of the two 2.5-inch drive bays inside the new Mini has been removed and replaced with a spot for the small PCI Express SSD cards that the rest of the Macs now use. This is fine for a single-drive or Fusion Drive configuration, but you can no longer install two hard drives and mirror the data for redundancy. As a result, the $999 Mac Mini Server configuration is dead.
That's a shame. I've never used a Mac Mini as a server, but lots of people do.