I think its dumb they couldn't have both software profiles available and be able to choose manual or auto, but the original mission did not call for autonomous undocking.
Boeing just didn't bother to make it so the mission could potentially be changed in-flight, they just decided they'll load a software profile on the ground and that missions will just never change.
Of course, this isn't to say that Boeing doesn't have much more serious problems going on, they clearly do.