A few points:

1) BFG states there is considerable variation in the degrees of automation from vessel to vessel. Baseline vessels use a lot of brute force in the place of automation for the systems where muscle power can do the job. Others are much more sophisticated. One of the selling points of a Lunar is that you can build it even in systems that can't support a real space industry. Obviously a ship built at Mars is going to have more sophisticated systems and automation than Feral Worldia VI. Space Marine vessels are described as highly automated with small, well trained, well equipped crews, which makes sense if their vessels are built at the more advanced shipyards.

2) The Eisenhorn/Ravenor books take place centuries before the timeline for the Calixus Sector/Koronus Expanse campaigns. Ciaphas Cain's career starts before it and ends after it. If the Koronus Expanse is "too far in the past" to represent modern 40K, so are half the 40K novels.