My hypothesis explaining three puzzling aspects of Starfarer. Forgive me if these have already been explained.
The idea is that flux is specifically gravitational fluctuations. The ship's reactor provides power by transmitting spatial manipulations across gravitationally shielded conduits. Normal transmission is in the form of solitons. 1. Entropy builds up in the system through the creation of standing waves at various harmonics. When these standing waves at peak push more energy into the capacitors than they can handle, they short out. Flux vents are specialized grav-wave dissipation devices, and the visual effect from full-on flux blowing is due to ragged space warps. Perhaps quantum foam amplification.
The reactor also uses this space-warping capability to travel.
2. Fleets slow down near planets because the space is already warped; there's backpressure.
Fleets slow down near other ships for exactly the same reason; the space-warping reactors interfere with each other.
Ships use a different engine for combat manoeuvring. 3. This is why travel speed and combat speed aren't simply proportional to each other. Also, it is how enemy fleets entangle each other - they intentionally emit gravitational noise to short out the delicate transportation space-warping process. (Similarly, the contrasting planetary slingshot interaction.) Perhaps defenders turn on the noise at the last moment, whereas attackers aggressively fire up the noise, interfering with their own space-warp manoeuvring, and thus part of the reason they have fewer ships available to deploy.
Anyway, I hope you enjoyed reading the idea as much as I did coming up with it.