The autoflaps logic is now part of the core Microsoft flight modeling, it's not done internally by the F-18 simulation. According to an explainations I've been given by Microsoft, it's a function of IAS, AOA and Mach.
It should be possible for airplane modedelers to get advantage of this feature that has been added in Acceleration, by adding autoflaps to any aircraft, but I don't know if it can be finely tuned.