I too have always subsumed inertial compensation into the operation of the maneuver drive.
Playing MgT 2e these days, where ship Power points have been brought back. I play that the Maneuver drive actually generates twice it’s rating, for example Thrust 2 (2G) as well as 2G for inertial compensation. So if the 2G M-Drive needs 20 Power, you could cut the grav plates and get an extra 10 Power out of it or up to Thrust 4.
It came about from trying to reconcile a Thrust 1/1G ship refueling from a 2G gas giant.
Obviously you reduce compensation for additional Thrust or Power at some risk to the crew. Vacc suits, acceleration couches/benches, G-drugs and the like all help the crew counteract the effects of uncompensated g-forces IMTU.
It's not necessary to have maneuver Gs > planet Gs to skim a gas giant.
Put the ship in an elliptical orbit (or, rather, a segment of one) with the perigee inside the atmosphere. This only requires thrust greater than aerodynamic drag (instead of greater than local G) -- keep the speed up and momentum will carry the ship back out of the atmosphere after the skimming pass. Atmospheric entry will be at hypersonic speed, and isn't a trivial task.
For MgT, it'd be Average difficulty check against Pilot skill to fly a safe skimming track (or use atmospheric operations rules).
Someone could assist through an Average difficulty Astrogation skill check to optimize the track (and there should be plenty of time available to bring the difficulty on this roll down quite a bit). Sensor ops, again at average difficulty, can also assist by forecasting "weather conditions" along the plotted skimming track.
Marginal failure indicates having to abort the skimming run with only half of the normal fuel load (either too high a track to scoop properly, or too low and it's necessary to climb out to avoid overheating the hull).
Average failure indicates having to abort the skimming run without collecting any fuel.
Exceptional failure indicates severe hull overheating or turbulence -- ship takes damage (I'm not confident in my understanding of MgT combat to figure out how severe it should be, but this should be a major crisis). Pilot skill check (no time modifiers allowed, stat is DEX) to mitigate damage, Engineer (maneuver drive) skill can assist by enabling maneuver drive overload operation to escape situation. Probably also destroys or at least damages the fuel purifier.
Of course, if the ship has enough maneuver Gs to hover, it can skim at subsonic speed and make this an Easy task.