If our ships really get dmg upon hitting the athmosphere with a high speed (devblog) i thought it might be good if that isnt just limited to the ship.
While asking for a complete inertia model, throwing people against walls when accelerating a construct is probably to much, i'd suggest a damage over time effect when players experience extreme accelerations. This dot would then be weakened by a certain degree if players sit in seats/benches while accelerating/decelerating, depending on the type of seat. A simply bench would only work for slightly to big accelerations, while special high speed seats could prevent that damage for very high accelerations.
This would add a bit of realism to the game and at the same time force people to design their ships with the required amount and class of seating opportunities.