Read his post again.
"In C# Aurora, commercial-engined and military-engined ships are treated separately. So if you have a fleet with mixed engine types that also includes ships with commercial and military jump drives, it will still carry out a standard transit if the respective jump drives are large enough for the ships with the matching respective engine types. However, if any ship with either engine type can't jump, the whole fleet will fail to transit."
This clearly indicates the intention to require civilian jump drives for civilian engines, and milspec jump drives for milspec engines.