There appears to be an additional hurdle with the temperature sensor. According to French site MacBidouille, Apple now uses the the harddrive's RS 232 interface to get temperature readings. Western Digital, Seagate and Hitachi all use slightly different connectors that are not compatible. So if your Mini ships with a Hitachi drive, it come with the Hitachi compatible cable. You can still put in a drive by another manufacturer, but won't be able to connect the cable to get temperature readings. As a result, it appears the the fan spins at max power all the time! It may be possible to use a tool like smartfan to manually get the fan under control, but if you want to use Apple's own fan control, you have to stick to whatever harddrive brand your mini ships with.
Haven't confirmed this myself yet, still waiting for my mini. I was planning on upgrading to one of those new Seagate Hybrid drives.