Gee Harliquin, I've understood the problem since 6 posts ago.
Please try this experiment. In spaceship mode, set your acceleration to 1LY/s while in a galaxy, with the default render settings and limiting magnitude of +8. Apply that acceleration constantly for 10 seconds of real time. After those 10 seconds, what should your velocity be? (10 seconds)*(1LY/s^2) = 10LY/s, right? Well, try it and see what you actually get.
Now repeat the experiment with the limiting magnitude set to +13. What do you find your resulting velocity is, then?
In physics, the velocity you have after some period of constant acceleration is your acceleration times the amount of time it was applied for. But in Space Engine's ship mode, that's not what you get -- the velocity you actually get depends on your framerate. That's why this does not work.
In order to make it work, you would have to calculate your "effective acceleration", based on what your framerate is. This is probably doable, except it will change depending on what's being rendered during your journey.