The optional movement system in MgT HG clearly shows spacecraft being pulled by gravity, as they would not be if they were equipped with agrav.
My conclusion: MgT spacecraft do not generally use agrav
Antigravity isn't necessarily the right phrase. Antigravity (in the sense of being unaffected by external gravity wells) is not necessarily the same as a Gravetic drive - meaning you generate your own gravity well and "fall" into it; the result of the latter will be an acceleration which is the sum of any 'real' gravity well and the 'artificial' one (which, in the case of an antigravity 'floating crate' or something, is zero acceleration either way). I agree that Mongoose has been deliberately vague about what exactly an M-drive is and how it works, but it clearly is gravetic.
From high guard - discussing reaction drives:
"The reaction drive takes the same space as a gravitic drive" - meaning that the conventional M-drive is gravetic.
A spacecraft might be operated with the Flyer(winged) skill, never the Flyer(grav) skill.
My conclusion: MgT spacecraft do not generally use agrav.
Observation: That is specifically for a streamlined ship. The point of being streamlined is the ability to behave like a modern aircraft or winged animal - i.e. following the laws of aerodynamics in order to be able to make more dramatic manoeuvres.
A flyer (grav) like an air/raft may be able to move in essentially any direction, but it's not unreasonable to assume it's going to handle like a high-tech analogue to a zeppelin, and a standard (non-streamlined) starship might well handle the same way. If you want to fly around like a jet fighter at supersonic speeds, you need to deal with airflow, and hence - I agree - you're either using thrusters or a manoeuvre engine which is locked forwards (which might as well be thrusters).
Gravetic propulsion works on an air/raft, and allows the thing to potentially reach orbit. Simply starting on the ground, setting the propulsion direction to "up" at 1.00001g and waiting will eventually put you at orbit altitude ("
Air/rafts can even reach orbit") with a minimum of fuss and effort (even if it takes a while), and if gravetic propulsion can work in atmosphere, there's no reason that gravetic starship drives can't.
(As an aside here, though, depending on how the 'gravity well' produced by the drive is perceived by air near to the ship you could produce some bloody weird turbulence around a ship under gravetic drive)
From the 1e core book discussing landing:
Any ship with a standard or streamlined hull may land on the surface. Unstreamlined ships suffer a –2 DM to any Pilot checks made in atmosphere while a ship with a Distributed hull suffers a –4 DM to any Pilot checks, and is likely to take severe structural damage if it lands. Landing at a starport is a Routine (+2) task for most ships taking 10–60 seconds
Since the skill remains a Pilot (spacecraft) check, one can assume the broad technology remains the same as for piloting it in orbit, whilst using aerofins and a streamlined hull with powerful forward thrust, combined with lifting surfaces dramatically changes the way a ship handles.