Remember that Autothrusters only work on ships with the Boost action. So only A's, TIE Interceptors, Star Vipers and Aggressors can really use them since they are a Modification. They may not be auto-include, but they are VERY good on those ships. I definitely think they are auto-include on the Aggressor for sure.
Love my IG-88 B&D build so far!
Jim