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How can the different 727-100 models be affected if they are all using the same aircraft.cfg, cs727100.air file and gauges from the panel folder

As far as I know, the aircraft.cfg is different. Same for the .air file. Actually is not cs727100.air, it is cs727200.air.
Air file contains all the coeficients used for the flight model.

Gauges are almost all the same, besides 1 or 2.