"Flux is also used for shields, and the ship needs to have at least half-decent shields, so the primary reason is just to keep the “shield flux per damage” number looking reasonably normal."
Why add a complicated "double flux for energy weapons" effect when you could just raise shield efficiency to 0.4? I don't think a simple 0.4 number looks less normal than reading a complicated effect on top of another already complicated effect, making it appear double nerfed and complicating mental calculations. And lore wise, just write that this ship specializes in the use of hyper flux efficient weapons and shields.