I think the disconnect/failure point between ...
1. economics suggesting that all ships should have a captain plus an all robot crew.
2. OTU rules, adventures, deckplans and color texts say 'it ain't so'.
... goes back to the difference between AI (as described in the robot books) and Self-aware robots (TL 17 in CT). Just because a robot is programmed to operate a ship like a pilot does not mean that it can actually replace a human pilot on the ship ... that would require the independent function that is reserved for TL 17 robots.
The automated factories that I have visited, still employ quality control people to examine the product coming out of the machines because the machinery is often perfectly willing to continue as normal if something unexpected happens. Newer machines can sense when something has gone wrong, but even they seem to generally default to 'stop the presses and call for a technician'.
Has anyone else encountered a Garmin or Magellan GPS that gives less than perfect advice? ... "Exit now would be a lot easier if this road had an exit here".

o:
So I could easily imagine a Robot Pilot that could handle the routine 'driving', like an aircraft on auto-pilot, or even be programmed for routine landings and takeoff ... but let the ship exit jump in an uncharted asteroid field and damage one of the stabilizers and the AI (non-Sophont) robot pilot will be perfectly willing to follow procedures exactly as programmed, right up to the point where the superfreighter collides with the highport.
Keeping a human pilot in the loop means that the robot pilot who exits jump in an uncharted asteroid field and damages one of the stabilizers, can detect that something has gone wrong and summon a sophont to make the decisions above its AI grade.
In terms of game mechanics, I respectfully suggest that 'minimum crew' (from Mongoose Traveller) must be sophonts, both by regulation and practical necessity, since a smaller sophont crew is potentially unable to deal with an emergency. The 'average' and 'full' crew numbers can certainly be filled out with AI robots capable of performing routine tasks and normal operations.
Thus in normal operating mode, the partially robotic crew is more cost efficient, but when a crisis strikes, the robots are of limited usefulness and the ship functions at one level lower ... a 'full' crew becomes 'average', an 'average' crew becomes 'minimal', and a 'minimal' partial-robotic crew may be insufficient to cope with the crisis (and thus illegal for any ship that carries mail or passengers).
Just some thoughts from IMTU.
YMMV