Not every crew goes through the merchants. Some PC's may have learned Astrogation in post generation to save on paying NPC's (or see below).
Regardless, imposing a -1 because someone also calculated the jump path is just dumb.
You've already admitted Astrogator is basically a non-job other than the calculations. Even you give them busy work at a barely skilled level.
This is what I am arguing. Not which particular spot your universe assigns them to.
You cannot assume that someone got astrogation via a career path. You have skills from connections and three of the campaign skills packages allow a player to get Astrogation-1.
The merchant comment was about commercial astrogators (aka NPCs).
Here's the reality. Traveller was set up around certain assumptions of task difficulty and crew requirements. These are fundamentally unchanged since 1981.
On the other hand, Mongoose keeps adding requirements, tasks, and difficulties to said tasks that are not reflected in the character creation system. It is moderately unlikely that a 2-4 term PC will actually qualify for the expectations of a commercial or naval position under mechanics in play.
Just for example, the Type S used to have a crew requirement of Pilot 1. Didn't need an astrogator or Engineer for a 100 ton ship. Free Traders didn't used to require Astrogators. Now they do.
I started a thread a few months back on the lack of support for the Astrogation skill. It nominally does a bunch of things with plotting courses and figuring stuff out. But there's nothing in the mechanics to make that a reality. No player with the astrogation skill is going to know what to do besides be the janitor, as you say. All that about the sensor tech/comms tech is part of real life naval navigators' jobs. But that's not mentioned anywhere explicitly in Traveller.
While Astrogators are probably unique in the "what does this job actually do?" category, Engineers are pretty f'ed too. They need Jump Drive, Maneuver Drive, Power Plant, Life Support, Mechanics, and Electronics to do the things their jobs require.
Your original point was that a hot rod ship was impossible because you can't meet the difficulty of the crew requirements. My point is that the rules as written a Skill 1 character isn't qualified for a commercial job if you take the task difficulties literally, even though they are intended to be. There are too many 8+ and 10+ Tasks involved. Astrogation is just the most egregious example.