ZFT, surely CAE and the like have a set software programme which they re-use for all types, weather, windshear and the like are not independent of type... surely then its just a case of modifying the linear equations of motion for each type depending upon the output from the flight model supplied by the aircraft manufacturer?
Most of the avionics boxes thse days in modern sims are the actual boxes used in the aircraft, with software supplying the data they would expect (position, tas, SAT, TAT etc).
I dont understand where the significant levy comes from, just because its a "new" type, especially civvy. The Graphics hardware and software will be the same. Ground handling would be the only thing I can think of that would require individual modelling (hence why a lot of sims dont do a great job of recreating ground handling).
I can completely understand why it gets expensive once you start throwing airdrop/Air to Air refueling and threat response into the mix, as these are highly type specific, for example, the interaction between AAR aircraft types and the aircraft require detailed modelling to recreate the complex aerodynamics that go on. I was surprised to see the Herc sim "simulates" the pressure wave and bumbling on the flight controls as you approch the AAR aircrafts wake... very realistic.