Ben,
Unfortunately, the 2007 manual does a very poor job addressing muffin fans. The
power distribution diagram seems to show them not needing a Spike. The Robot section of the manual only specifies what gauge electrical wire to use with them. Based on the power distribution diagram I would say FIRST is allowing the direct connection to the breaker panel.
As far as your bad experience in 2003... If the muffin fans on the Victors are directly connected to the breaker panel I don't see why other muffin fans shouldn't be. It's unfortunate not every regional can have a lead inspector who's a FIRST veteran and also an electrical engineer.