Bridge Commander unfortunately isn't designed around realistic spaceflight or combat physics, even if you crank up speeds and acceleration values.
There's no real physics simulation under the hood - everything (movement, weapons, targeting) is heavily abstracted and tuned for gameplay at relatively short ranges.
Weapon ranges in particular are hard-limited. Phaser range is effectively capped (around the ~100–120 km mark you're seeing), and that limit isn't exposed to scripting. As far as we know, increasing it would require engine-level modification (hex/memory patching), not something you can adjust via standard modding tools.