This same base capsule design is also supposed to operate autonomously. It previously attempted an autonomous docking. The code was written, it was approved for flight previously. It is not like "autonomous docking" was never a part of the specification for this model of craft; it just wasn't the expected process for this particular mission.

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.