I don’t think adding autonomy is all that expensive. You need almost all of the stuff anyway, since no pilot can fly a spacecraft by the seat of their pants. As I mentioned in an edit (which you may not have seen when you wrote this), the Shuttle was unique or nearly so in not being crew-optional.

I was thinking of this from the other way around, of adding piloting capabilities to an autonomous mission; you now need to adding a bunch of specialized equipment to keep the meatbags inside the spacecraft happy. I’m not sure which way the Soviet shuttle was designed: primarily human-piloted, with optional autonomy added as an afterthought, or meant to be pilotless but with people were added later. It’s the latter case I was concerned about, but I realize now that you’re talking about the former.

I don’t think anyone has designed a pure cargo craft and then tacked on crew capability. The requirements for a crew are so big (you need a substantial pressurized volume, life support, the ability to renter and land, etc.) that I don’t think it would be practical.