Well, trying to use realistic physics calculations against such unrealistic physics is only going to give nonsense answers.
For example, travel is done in 5 second steps. Non missile weapons hit on the same round they are fired, so in a sense, they travel instantly.
F=MA. Mass is a known quantity (we'll ignore the bizarre relativistic effects on mass). But acceleration? It's infinite!
The same this with the ships themselves. They can go from 0 to 16000 km/s in an instant. You can't apply real physics to this, because all your answers are going to be zeros and infinities.
That's not to say the lore couldn't be adjusted to be more compatible with real physics without really changing the underlying simulation. But it'd be a lot of work, and then you'd actually have to code the damn physics too.
Speaking of lore, there's something that bothers me about it. If these trans-newtonian elements have existed all along in the earth's core, along with lots of other stellar bodies, why are those bodies following newtonian physics? Why isn't the earth slowing down as it orbits the sun due to the drag of the trans-newtonian elements against the viscous media that makes up the dimension they're partially in?
Also, as wonderful as trans-newtonian tech is in many ways, it would be nice to be able to build fully newtonian ships, for things like very long distance scouting. In real life, you only need to apply force to accelerate. Object in motion stays in motion and all that. So if I want to shoot a probe over five systems, it'd be nice to only have to use fuel to adjust trajectory and accelerate. Of course... the fuel itself is made of a trans-newtonian element...