Military flight time is just computed differently. Flight time is computed from wheels up to landing. Most military sorties are training in nature, there isn't ever any "dead time" or cruising on a military training flight.
As far as Spirit goes, the 3000TT is a nod towards military flight time conversion. It's less than civilians are required, but still not an outrageous amount. 3000 hours for a military pilot (transport, not fighter) is about right for a career military pilot. I don't think the mins are unfair at all.