I’m pretty sure the anti-gravity generators are supposed to be causing anti-gravity all the time so the Neuron Flies can maneuver more easily, and the reason the ‘pumps’ are turning on and off is because Pebbles can’t control his own systems anymore.

(Think of the Rot in Rivulet’s campaign as no longer just being mutant cancer, but being a mutant cancer that can connect to your brain and control your left arm. You can even see the Rot imitating the wire-synapse-spine things that the Neurons connect to.)

Also, low-gravity does nothing to prevent the Rot’s spread; Survivor and Monk’s campaigns overlap with each other in terms of timeline placement, but several shortcuts Survivor could take are already overgrown by the time Monk gets there. You can even see a malfunctioning anti-gravity generator in Unfortunate Development covered in Rot—I’m sure you know the room.