So...it's been years since I've been active on this forum. But one thing I do remember feeling and thinking about a fair bit was how the missions in Part 1 (where you play as Samuel Bei) felt a bit held back by the fact that you're still piloting the same fighters as you did in FS2, save for the Aurora (and, of course, the missions where you use Vishnan strike craft, which was really damn cool), especially on the missions where you're doing a similar kind of thing that you were in FS2, where you needed to cover lots of distance in too short of a time.
Add on to the fact that you can only use any of the new Tev fighters in one mission of War in Heaven, and that mission being what it is, the lack of repair ability really hurts the viability of using one of them.
So: why not allow for the new Tev fighters in the Part 1 campaign? Since you're playing as the GTVA in that entire campaign, that seems like an excellent way to give the players the chance to enjoy the new fighters (which are really fun to fly/use) when you basically can't do that in the War in Heaven campaigns (and War in Heaven has its own slew of new fighters/bombers, too).
While balance is something of an issue, the player can always increase the difficulty, and each of the new generation of strike craft still has its own serious limitations--the Atalanta has very limited utility against warships and is severely lacking in secondary flexibility, the Nyx is slow and not very maneuverable, and the Draco's armament only as strong as the Perseus. And, of course, you'd still be using the old bombers in missions where you need that.
It would also make sense, lore-wise, for the battlegroup to have them, since they're supposed to be the best of the best to have the best possible chance to pull off the Tev's plan to conquer Sol.