To go faster, you add more thrust, so the extra speed would be related to whatever generates that thrust. IDK, maybe you could say zero flux boost is converting extra energy that had been used for something else (shields maybe?) into thrust, so it is a flat value based on how much extra energy you have? Why would a percentage make more sense to you? A percentage of what?
At the end of the day, the game is basically naval combat re-skinned in space. It's like starwars re-skinning atmospheric combat in space. It's not even vaguely realistic, so there's no point in picking through the minutia.
1. In Star Trek, when they want their ship to move faster they divert (all) power to the engines from the weapons/shields. SS's flux system, including the 0-flux boost, reminds me of that.
2. Although I'd be looking at acceleration in a system with no max speed, SS has max speed, so I would instead use +percent max speed, like Helmsmanship's level 2 effect.
3. Good analogy to Star Wars and reskining atmospheric combat, haven't hear that one before. For SS, I've heard "tanks on ice", and naval combat (but more maneuverable) and phase=submarines. The existence of hyperspace storms further supports the naval combat reskin argument.
4. As for picking apart and analyzing the internal workings of works of high fantasy or "video-game logic" being a fool's errand, I've found it's important to understand why a designer designed their system/product a certain way if your intent is to (criticize or) modify that system/product. Not necessary, but often useful enough for me to be a worthwhile endeavor in the pursuit of (criticism or) modification.
5. Thinking about the in-game descriptions more, travel occurs mainly in hyperspace with occasional hyperspace (deep) along with the existence of the hyperspace storms, rather than in standard space, so there's already an in-universe catch-all for the non-standard mechanics of interstellar travel. I'd assume this is why systems and planets take so little time to travel between. Because the fictional characters found out about hyperspace's existence, and how to enter it from what I'm assuming is standard space, and because travel is so much faster in hyperspace, people only re-enter standard space when needing to interact with planets. As in SSeth's Cowboy Bebop analogy, which may be a weak analogy because Bebop has a lot of non-hyperspace combat.