My problem with that is that it still makes not much sense.
If my Scout Courier (with 'ship' controls) can fly through an atmo and land and a Ship's boat (with 'boat' controls) can fly through atmo and land, why are they different? You could certainly fit the same controls in either ship.
Also, Pilot skill does not, as such, relate to astrogation/navigation for jump. You have to fly a setup path perhaps, but that's a mundane feat (you have to fly approaches to planets, to orbits, to stations, etc. so this is not different). That's why we have Navigation/Astrogation. And small craft and small ships both have to fly the same approaches.
I see this as another flavour thing (much like 'pick a specific sword or gun and don't get any benefit with similar weapons'). I don't see it as making much sense.
Now, MT, for instance, makes all vehicles mostly built by the same chain of steps. And starships and non-starships can both have the same control types. So in that setting, there's even less differentiation.
And really, if you are not expected to fly out of atmo envelope with most small craft (or not farther than an orbit), then why aren't they just grav vehicles, because that's what many grav vehicles can do and likely use the same contra grav most of the time....
The silliness is:
Aircraft/Air Raft/Grav Vehicle + Small Craft + Pilot - there's a lot of commonality here that makes little sense because of the need to fly the same types of approaches.
To look at Earth analogs:
The military has different control sets than civilian planes (more stuff), but if you can isolate the flying parts, and you are flying the more mundane military craft (not carrier launches perhaps), you could probably fly one of them if you knew how to fly a similar civilian plane. You might have troubles with the instability of interceptors (which make them hard to land safely) or the heavy weight of some weaponry (A-10 pilot?), but you could probably manage around it if you were a good pilot.
And flying an approach to an airport is something all pilots learn. Similarly, anyone going to orbit, going out of envelope, or intra system, or landing on planets, or docking with stations would have to know the same sorts of stuff. The specifics of the manipulation of the vehicle vary somewhat (to accomodate for ponderousness and mass or other considerations) but there is a lot of commonality.
Really, every 'drive' skill including small craft and pilot could exist under a Vehicle cascade.
In MT, they had small and large watercraft, air cushioned vehicles, and small personal watercraft. For aerospace, they had fixed wing, jet, helo, personal aircraft, lighter than air, and they maybe ought to have ground-effect (WIG). Then they had Ship's Boat and Pilot.
The interesting thing about the plane analogy there is Jet is Jet. It isn't large jets and small jets, or single engine jets vs. multi-engine jets, or civilian jets vs. military jets. In the real world, those are different qualifications.
That may be one of the things the rule-set is missing:
Qualifications on equipment - and for bigger equipment, that could take a lot longer. While unqualified, you may have some significant penalties to handling that model because you don't know its particulars. Thus a single engine jet pilot could likely pilot a multi-engine pilot but he might be quite rough because he's never flown one and never qualified (to understand the
differences in handling, emergency actions-on, etc). He knows how to fly so he might also be able to fly a prop plane, but it too would be something he should qualify on first to avoid pitfalls.
Traveller worried about TL differences, but model differences/capability differences of vehicles actually may be at least as much of a challenge.
I feel like I haven't found a good solution for grav vehicle/ships boat/pilot yet, but I've tossed a lot of flavours around.