NASA may be taking a different approach, but in civilian aerospace it is prohibited to have code that doesn't run or doesn't trace to a system requirement. I assume that was their rationale for removing it.
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.