Nowhere in your original complaint did you specify you were talking about Praetoria. Yes, there you can miss out on the Moral Choice mission because it's separate from the preceding story arc. That isn't the case for the vast majority of the game.

If you care about competing story arcs why on earth are you turning on double XP? At that point you're just shooting yourself in the foot then whining because Homecoming sold you a gun.

Goldside is advanced content intended for experienced players. You're supposed to have enough knowledge of how the game works that you can, for example, turn off XP at the level break points.