One intriguing characteristic of "inertial damping" aboard starships we witness a lot in TOS and the later shows is that even if one part of the ship shakes, not every part needs to.
This makes a weird sort of sense. The damping is supposedly achieved by projecting some sort of a stabilizing field, and we have seen that artificial gravity fields are specific to individual rooms. Just because the field on Main Bridge is getting a punishment doesn't mean that the field on Sickbay would fail to a similar degree and leave McCoy with a floor covered in broken glass, or that the field on Transporter Room Four would let the Genesis Device tip over.
Another possible explanation for the fact that bottles never fall from tables even when Ensigns fly across the Bridge is that certain horizontal surfaces, shelves etc. have their own low-level gripping fields. Enough to stop a 1.1 kg bottle, nowhere near enough to hold still a 100 kg Security goon. Naturally, the Genesis Device would have such a gripper of its own, increasing the efficacy and providing stability even in demanding conditions.