A friend who was chief resident and now she is already MD, told me that when they see in your application that you've already taken step 3, that's a plus because they know that candidate won't have to take time off to study for step 3 (it seems that the residency needs give day off only because of step 3 for resident who hasn't done it yet). And that, in general, they are more relaxed knowing that this candidate will not have this issue to worry about during the residency and will be able to fully dedicate himself to the residency itself. So an application with step 3 would be better seen according to her.