If you have Pilot skill, does this change in HG mean you don't generate Ship's Boat for characters? I don't think so.
And you are right about Pilot's often (but not always) moving up in increments; I know one who went directly to learn how to fly multi-engine jets at a School in Australia. That said, if you can fly a multi-engine jetliner, I'm quite sure you can fly a Ship's Boat.
----- if you looked at this beyond canon ----
What makes more sense?
Categorizing skill into vehicle types (watercraft, aircraft, etc - perhaps sm watercraft, lg watercraft, etc as MT) or into the skills required to operate them (Nautical Pilot)?
Let's look at some muddy profiles:
a) Ship's Boat - can fly small craft, including anywhere in the system they can reach, including flying liftoffs, landings, dockings, various approaches through traffic, etc. - this suggests sensors, comms, etc. as well as a user (someone who can use some position determining gear and a basic digital radio plus a basic passive or active radar). You can go to orbit and enter and orbit and beyond to anywhere in the system (fuel and life support permitting). Can do fuel skimming in the right small craft.
Tech wise: Depending on the Trav Version, controls, sensors and comms can be the exact same as starships have. The small craft will use contra grav and thrusters of some sort (thruster plate, or ?), some fair amount of computer / nav software is required for orbital trips as is some kind of life support.
b) Grav Vehicle/Air Raft - can fly grav powered vehicles that are not considered small craft, but that are powered by contra-grav, including liftoffs, landings, dockings, traffic approaches, etc. and that can certainly get to orbit (and the sensors/comms/etc comment above applies here) and presumably could enter an orbit
Tech wise: Depending on the Trav Version, controls, sensors and comms can be the exact same as starships have. The grav vehicles will use contra grav, some fair amount of computer / nav software is required for orbital trips as is some kind of life support.
c) Pilot - can fly 100+ dTon ships (which might only be 1 dTon heavier than a 99 dTon small craft) and can fly liftoffs, landings, dockings, various approaches through traffic, etc. - including entering and exiting orbit, fuel skimming from gas giants, entering and leaving orbit, travelling around the system, and flying an approach given to you by the navigator to line you up for jump entry. And note that system ships of 100dTons go here and they have *no jump related aspects*.
Tech wise: Depending on the Trav Version, controls, sensors and comms can be the exact same as small craft or vehicles have. The spaceship will use contra grav and thrusters of some sort (thruster plate, or ? - M-Drive), some fair amount of computer / nav software is required for orbital trips as is some kind of life support. Fuel skimming is possible with the right gear. There could be a jump drive present (or not for system ships) but most of that is owned by the engineer and the navigator with the pilot doing very little (fly a provided approach vector).
d) Astrogator/Navigator - does the jump calcs, checks them twice, looks for numbers that are naughty or nice... and feeds the numbers to his pilot and maybe some to his engineer.This guy does the head-hurting math (well, moreso than in-system travel but even that could be head-hurting too). THIS is the guy who does the jump work, not the pilot, who only flies a directed vector prior to jump.
So, A, B, C have at least a 2/3rds overlap in capabilities. It seems a stretch to me that we need 3 skills for that. You can make a justifications to fit RAW (rules as written), but if you were designing a game from scratch and you knew you wanted a streamlined skill list, it seems pretty likely 3 skills here is overkill.
Looking at this list, it really feels to me if I was designing a game, I'd be looking for a way to put these three skills together.
There have been some games that said "if you know system/ship/weapon X, you may treat system/ship/weapon as having skill level of X - 1".
For ships, this might make real sense if you want detail. A 50K dTon agroproduct hauler that has no atmo capabilities and runs only with refined fuel and no jump is vasly different than a torpedo fighter with no jump, crazy Gs of accel, lots of weaponry, and is super manouverable which is different again from a 300 dTon trader with jump drive, fuel scoops and purifying gear, and that is very streamlined for landing on frontier planets.
In some campaigns, I've provided players with lists of what gear they know. I've then made calls in play about how similar that gear is to what they know such that their skill may apply with a penalty.
I mean, if you know how to fly a contra-grav grav vehicle that happens to be 50 dTons to orbit safely, you can likely do the same with a 100 dTon spaceship. But you may never have skimmed fuel nor learned how, nor would you necessarily be good at world to world travel without some additional training time. It's hard to boil that all into a single omnibus skill but equally hard to make sensible 3 different progression trees.