I think this is a brilliant explanation for the design of the XBoats. It doesn't explain why the XBoats would be routinely manned. Maybe they wouldn't be - I'm not aware of anything in CT that addresses the question.That brings up a point of Cart vs Horse ... ROUND 1 ... FIGHT!
Designing an XBoat for automation isn't the issue (because it already is, by default).
You want to have quarters for up to 2 people on board so that the XBoat service can be used as an emergency transport system for highly sensitive cargoes and personnel (an example of vaccines is given in S7). By having habitable space aboard, the IISS can even use XBoats to move personnel around when issuing post reassignments and/or when mustering out of the service at the end of a career. Granted, an XBoat is no passenger liner, but it ought to be capable of carrying "precious" people and "precious" cargo (in limited quantities!) when needed ... in addition to the baseline capability of carrying communications between star systems.
Designing the system such that only "specialized" XBoats have the capacity to carry crew/passengers/cargo would be self defeating, since by their very rarity those "extra" transport services will always wind up being in short supply exactly when you need them (go away, Mr. Murphy!). The logistics of needing to manage two types of XBoats just isn't worth the expense of NOT having the capability to transport crew/passengers/cargo when you REALLY need to in a crisis situation. Better to just streamline everything on a standardized design that has the pressurized life support capacity built into it every single time so it's there whenever you might need it.
Because that's the thing about emergencies.
They rarely give you enough advance notice to get all your logistics "just so" and perfect in time to meet the needs of the emergency. Best to have the capacity built in from the start.
One of those "you always fight with the forces you have" kinds of deals, rather than wish casting for the forces you WISH you had to meet the moment.
I can easily imagine that there have been plenty of times (i.e. more than can be conveniently counted) in the history of the IISS between IY 800-1100 when the fact that the standard XBoat design is one that can carry a Middle Passenger plus 1 ton of Cargo has proved critically pivotal to the outcome of all kinds of time sensitive crises on plenty of worlds inside the Third Imperium. Even if it's a case of "1 world per year" out of the 11,000+ worlds within Imperial borders, that's still amounts to some 300 worlds that would have had a different outcome if the passenger+cargo option was not available in a time critical way during a world crisis.
Sure, it might cost a little extra relative to a purely automated drone service with no life support on board ... but when you measure that slight surcharge in XBoat fleet construction, operations and maintenance costs against the value of WORLDS SAVED by having that otherwise superfluous capacity built into every XBoat, you're suddenly talking about shaving pennies at the expense of financial stability for entire banking systems.
I don't find the "human crew to protect against boarders" explanation to be convincing - one crewmember with some small arms wouldn't provide much protection against a determined boarding attempt. For that matter, if I were a pirate trying to get the XBoat, ideally I'd have a Corsair type ship (ala The Spinward Marches Campaign) to take the boat onboard and then move someplace private to deal with it. Failing that, I'd just tow it somewhere where I could deal with it. Rather than attempt boarding, I'd penetrate the hull to depressurize the ship (hopefully killing the crewmember). Voila - XBoat secured.
Unless the XBoat's point of exit from jumpspace is predictable (which it must be if turnarounds times of hours are routine), then the armed tender will be close at hand, and small arms to defend against boarders are completely unnecessary.
Or if you're worried about misjump. But there would be very big worries in this case - the ship might come out of jump space in interstellar space, in which case it would be stranded - unable to make another jump, and unable to even accelerate to a velocity that would get the boat to a star in years. Or, you might jump into an unplanned system. In this case, the pilot could contact the local authorities and request assistance, possibly more effectively than an automated ship could. Still, the remote possibility of a misjump seems a small reason to require all the thousands of XBoats to be manned by pilots who must endure a week of solitary travel to do approximately nothing at either end of the trip.