RogueBanshee,
You are too concerned with why the Intrepid is part of Confed. The fact that nobody knows why it happened, doesn't mean that it didn't happen. If I walked outside and somebody has a gun and is shooting folks, I'd probably be at a loss to tell you why he's doing it, but it wouldn't change the scene infront of me at all. Same thing goes for the Intrepid. No matter how illogical or ludicrous it may seem to you that the Border Worlds whould give the ship to Confed, the fact that Confed HAS possession of the ship at the end of WCIV indicates that they did so.
Now my guess is that the Union and Confed signed a treaty, and that in a broad stroke looks like the following: It limits that Union's navy, in exchange for recognition as a state by Confed. Confed pledges a non-agression pact with the Union, and agrees to some limited defensive duties (I'm very curious about how the Union feels about Confeds withdrawl during the Nephilium conflict). Everybody gets something out of the deal, but the Union is still the small time player, and Confed holds the upper hand materially if not morally at the end of WCIV. The Union wants it's freedom, and Confed is willing to grant it, but not unconditionally, if they push too hard Confed walks away and they really do end up fighting a terrible war that they almost certainly couldn't win in any conventional way. Yes they might be able to fight Confed long enough and tenacious enough to eventually get Confed to withdraw, but they'ed always be under pressure from the Confederation. Really agreeign to giving up the ship could be just as simple as taking a course where everybody wins (peace for Confed, Freedom for the Union) rather than one where everyone loses (war). I just can't see the Union throwing away millions of lives over keeping the crappy old Intrepid and getting to build it's own fleet, especially considering that Confed, despite its faults, has never looked like the sort of organization that would fail to honor it's treaties. Maybe I misjudge them but on a whole I trust the Confederation government's word in foreign affairs. All of this is of course conjecture and irrelavent to the fact that the BWS Intrepid is returned to Confed after WCIV as per the winning path ending.
-Starcrunch