Why, because put simply, the whole idea behind the Freespace Port was to re-create "Descent: Freespace" the game (and to a lesser extent, "Silent Threat"), in the "Freespace 2" engine. They have done some cosmetic upgrades, and some non-cosmetic upgrades... such as the Lucifer's beams, and the addition of the mission after you jump into Sol. However, the main thing to preserve from the original is the gameplay. Now, there are a few issues that can't reverted to the original, such as the "big dammage" flags on capital ships (so you can't Prom the Hades to death), but having a weapon with different dynamics than the original, unballances things to an extent that its not realy the same campaign. I mean, if the PromS is better than the Prom-O, and someone says "why not stick with the PromS, since its a better weapon", I say (sarcasm engaged) "Why not give us the Kayser too, or the Maxim. I know I'd have liked to mount a bank of Maxims when engaging the Lucifer in hyperspace, where sheilds are ziltch." (Sarcasem dis-engaged). If we change things so that something from later in the story, is available earlier, that's breaking cannon, and that's a no-no. Granted, "ST:R" is a re-write of "ST", but I don't think it will be considered a cannon campaign... even if it is better.
That's my 1.6 cents US (2 cents Canadian) on the issue.