I think what Deathsnake wanted to say is that there is no need for a separate .exe because you can do all that stuff you mentioned with the one that is already there. You can make your mod for Saga much more easily to install and play (and make your mod smaller because of no redundant assets) if you just mod the game instead of producing another total conversion. After all it is rather likely that your target audience has Saga installed already.
The players would just use the button "mod" in the Saga launcher and you get your own main hall, intro, menus and all that stuff. :)
I don't know how much Saga deviates from Open Freespace, but you should be able to create your own Enigma shortcut that starts your mod directly if you don't want any "WC3+4" (Saga launcher) visuals to distract from your WC1+2 experience.
As to FRED, this is so much fun!
Well of course its a mod, as its a development of the Freespace Engine and what Saga already built. What I mean is how easy would it be to create a separate .exe for Eagle Rising?

Why would you want to build a separate game if you are using our assets anyway? ;)
As to FRED, this is so much fun!
It definitely is. I'm really tired today because I messed around with FRED last evening quite a bit.
My main problem is that I have too much fun seeing cruisers blow stuff up, for example a group of transports or a starbase. I can watch that for hours. (which I did yesterday)

But at least I figured out how to do asteroid fields, some backgrounds with huge planets and suns and so on, patrol routes, mission objectives based on destroying things, setting cargo and how to enable scanning, how to end the mission when landing on a ship and some other basics of the editor.

I even did a small mission where you start from a star base, scan some freighters finding the one with the drugs and then it becomes hostile and you have to disarm it so it will give up. Then you land. End of mission. Simple but you can learn a bit about triggers, objectives and stuff.

I just had some weird effect that the ship I was supposed to land on became some sort of ghost I could fly through. No idea what I did wrong but whatever.

Hmmm.. Maybe I will make a FRED thread here and post what I am doing. I'm a FRED beginner myself so maybe if I post some things I find out in FRED I can inspire other users to try that as well and everybody learns something in the process. Of course real FREDers will laugh about us but maybe we will have some fun.
I already have another one:
Is it possible to make those giant plasma cannons on the capships workable? Is it enough to create a powerful gun in the weapons.tbl or would the hardpoint have to be specified in the .pof?