I am not sure, if someone already has mentioned this wish: It would be fine, if the aircraft specific configuration files would be additive to the standard config file. This means, that you can manage all your global settings, which are the same over all aircrafts, in the master config file and only the special settings necessary for a single aircraft must be set in the specific config file.
Therefore it's only necessary, that FSFK reads the standard file and override all settings found in the specific config file. This change is possible without losing compatibility. So if one has a full blown config file it overrides all settings of the standard file - fine. For files with only few settings only these settings are taken and the rest of the standard config stay untouched - also fine.
This improvement will make it much easier, to change global policies.