My guess is they had to do this or else you would have to set the analogReference in each sketch in the setup section. This way they were able to set the power on default to DEFAULT so you wouldn't have to use analogreference by default.
I think this is the exact reason why the deferred change of reference was chosen.
You could argue however that when analogReference is actually called, the function should change the reference before returning. If you think this is a better approach, you could post a change request accordingly.